NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1907156703|ref|XP_036020161|]
View 

msx2-interacting protein isoform X6 [Mus musculus]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
SPOC_SHARP cd21543
SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor ...
3056-3216 1.66e-97

SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; SHARP, also called Msx2-interacting protein (MINT), or Spen homolog, is an estrogen-inducible transcriptional repressor that interacts directly with transcriptional corepressors silencing mediator for retinoid and thyroid receptor (SMRT)/nuclear receptor corepressor (NCoR), histone deacetylases (HDACs), and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also called RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain that binds to SMRT/NcoR. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


:

Pssm-ID: 439206  Cd Length: 163  Bit Score: 311.45  E-value: 1.66e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3056 KYPIVWQGLLALKNDTAAVQLHFVSGNNVLAHRSLPLSEGG---PPLRIAQRMRLEASQLEGVARRMTVETDYCLLLALP 3132
Cdd:cd21543      1 RYPVVWQGLLALKNDEAAVQMHYVSGNQDLAKRSLPRHLTNgnlPPLRIAQRMRLEPSQLEGVARKMQDESEYCLLLALP 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3133 CGRDQEDVVSQTESLKAAFITYLQAKQAAGIINVPNPGSNQPAYVLQIFPPCEFSESHLSRLAPDLLASISNIsPHLMIV 3212
Cdd:cd21543     81 CGRDQEDVLKQTNNLKNGFITYLQQKQAAGIVNVPNPGSQQPAYVVHIFPPCEFSNSHLSRLAPDLLNSIADI-PHLMIV 159

                   ....
gi 1907156703 3213 IASV 3216
Cdd:cd21543    160 IATV 163
RRM4_SHARP cd12351
RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
107-183 8.19e-47

RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


:

Pssm-ID: 409787 [Multi-domain]  Cd Length: 77  Bit Score: 162.93  E-value: 8.19e-47
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703  107 FGKSMPTNCVWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDF 183
Cdd:cd12351      1 FGKSMPTNCVWLDGLSENVTEQYLTRHFCRYGPVVKVVIDRQKGMALVLYDEVECAQAAVKETKGRKIGGRKIQVDF 77
RRM3_SHARP cd12350
RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
33-106 3.44e-45

RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


:

Pssm-ID: 409786 [Multi-domain]  Cd Length: 74  Bit Score: 158.34  E-value: 3.44e-45
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907156703   33 ATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLG 106
Cdd:cd12350      1 ATRTLFIGNLEKTTTYGDLRNIFERFGEIIDIDIKKQNGNPQYAFLQYCDIASVVKAIKKMDGEYLGNNRLKLG 74
PHA03247 super family cl33720
large tegument protein UL36; Provisional
1201-1635 1.62e-10

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 67.66  E-value: 1.62e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1201 PETHPKTPEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAgekPAEPAPVSEETKLVSEPASV 1280
Cdd:PHA03247  2571 PRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPP---PPSPSPAANEPDPHPPPTVP 2647
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1281 PVEQPRQSDVPPgedsRDSQDSAALAPSAPQESAATDAVPCVNAEPltpgTTVSQVESSVDPKP------SSPQPLSKLT 1354
Cdd:PHA03247  2648 PPERPRDDPAPG----RVSRPRRARRLGRAAQASSPPQRPRRRAAR----PTVGSLTSLADPPPppptpePAPHALVSAT 2719
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1355 QRSEEAEEGKVEKPDTTPSTEPDATQNAGVASEA-QPPASEDVEANPPVAAKDRKTNKSKRSKTSVQAAAASVVEKPVtr 1433
Cdd:PHA03247  2720 PLPPGPAAARQASPALPAAPAPPAVPAGPATPGGpARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRES-- 2797
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1434 kseridreklkrSSSPRGEAQKLLELKMEAEKITRTASKSSGGDTehPEPSLPLSRSRRRNVRSVYATMT-------DHE 1506
Cdd:PHA03247  2798 ------------LPSPWDPADPPAAVLAPAAALPPAASPAGPLPP--PTSAQPTAPPPPPGPPPPSLPLGgsvapggDVR 2863
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1507 SRSPAKEPVEQP---------RVTRKRLERELQEAVVPPTTPRRGRPPKTRRRAEEDGEHERKEPAETPRPAEGWRSPRS 1577
Cdd:PHA03247  2864 RRPPSRSPAAKPaaparppvrRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPL 2943
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907156703 1578 QKSAAAAGPQGKRGRNEQKVEAAAEAGAQASTREGNPKSRGEREAASEPKRDRRDPST 1635
Cdd:PHA03247  2944 APTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSL 3001
PTZ00121 super family cl31754
MAEBL; Provisional
213-844 8.81e-10

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 65.16  E-value: 8.81e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  213 RREERRGSYEY--SQERTYYENVRTPgtypEDSRRDYPARGREFYSEWETYQGEYYDSRYYDEPREYREYRSDPyEQDIR 290
Cdd:PTZ00121  1189 KAEELRKAEDArkAEAARKAEEERKA----EEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFE-EARMA 1263
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  291 EYSYRQRERERERERFESD--------------RDHERRPIERSQSPVHLRRPQSPGVSPAHSERLPSDSERRLYRRSSE 356
Cdd:PTZ00121  1264 HFARRQAAIKAEEARKADElkkaeekkkadeakKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKK 1343
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  357 RSGSCSSVSPPRYDKLEKARlerytKNEKADKERTfdpERVERERRIVRKEKGEKDKAERQKRKGKAHSPSSQPSETEQE 436
Cdd:PTZ00121  1344 AAEAAKAEAEAAADEAEAAE-----EKAEAAEKKK---EEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAA 1415
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  437 NDREQSPEKPRGSTKLSRDRADKEGPAKNRLELVpcvvltRVKEKEGKVIEHPPP---EKLKA-RLGRDTTKASALDQKP 512
Cdd:PTZ00121  1416 AKKKADEAKKKAEEKKKADEAKKKAEEAKKADEA------KKKAEEAKKAEEAKKkaeEAKKAdEAKKKAEEAKKADEAK 1489
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  513 QAAQGEPAKSDPARGKALREKVLPSHAEVGEKEGRTKLRKHLKAEQTPELSALDlEKLEARKRRFADSGLKIE-KQKPEI 591
Cdd:PTZ00121  1490 KKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAE-EKKKADELKKAEELKKAEeKKKAEE 1568
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  592 KKTSPETEDT---RILLKKQPDTSRDGVLLREGESERKPVRKEILKRESKKTKLERLNSALSPKDCQDPAAVSAGSGSRP 668
Cdd:PTZ00121  1569 AKKAEEDKNMalrKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKK 1648
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  669 SSDVHAglgelthgsvETQETQPKKAIPSKPQPKQLQLLENQGPEKEEVRKNYCRPREEPAEHRAGQEKPHGGNAEEKLG 748
Cdd:PTZ00121  1649 AEELKK----------AEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKA 1718
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  749 IDIDHTQSYRK-QMEQSRRKQrmEMEIAKAEKFgspkkDVDDYERRSLVHEVGKPPQDVTDDSPPSKKRRTDHVDFDICT 827
Cdd:PTZ00121  1719 EELKKAEEENKiKAEEAKKEA--EEDKKKAEEA-----KKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEK 1791
                          650
                   ....*....|....*..
gi 1907156703  828 KRERNYRSSRQISEDSE 844
Cdd:PTZ00121  1792 RRMEVDKKIKDIFDNFA 1808
PHA03247 super family cl33720
large tegument protein UL36; Provisional
2521-3046 1.14e-07

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 58.41  E-value: 1.14e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2521 PANLGPTLTPHHPPALP------------SKLPAEVNHVPSGPSTPADRTIAHLATPKPDTHSPRPTGPT-------PGL 2581
Cdd:PHA03247  2512 PSRLAPAILPDEPVGEPvhprmltwirglEELASDDAGDPPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAvtsrarrPDA 2591
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2582 FPRPCHPSSTTSTALSTNATVMLAAGIPVPqfissiHPEQSVIMPPHSITQTVSLGHLSQGEVRMSTPTLPSITYSIRPE 2661
Cdd:PHA03247  2592 PPQSARPRAPVDDRGDPRGPAPPSPLPPDT------HAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPR 2665
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2662 TLHSPRAPLQPQQiEARAPQRVGTPqPATTGVPALATQHPPEEEVHyhlPVARAAAPVQSEVLVMQSEYRLHPYT----- 2736
Cdd:PHA03247  2666 RARRLGRAAQASS-PPQRPRRRAAR-PTVGSLTSLADPPPPPPTPE---PAPHALVSATPLPPGPAAARQASPALpaapa 2740
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2737 ---------VPRDVRIMVHPHVTAVSEQPRATEGVVKVPPANKAPQQLVKEAVKTSDAKAVPAPAPVPVPVPVPTPAPPP 2807
Cdd:PHA03247  2741 ppavpagpaTPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPP 2820
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2808 HGEARILTVTPSSQLQGLPLTPPVVVTHGVQIVHSSGELFQEYRYGDVRTyhAPAQQLTHTQFPVASSISLA-SRTKTSA 2886
Cdd:PHA03247  2821 AASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRS--PAAKPAAPARPPVRRLARPAvSRSTESF 2898
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2887 QVPPEGEPLQSTQSAQPAPSTQATqpiPPAPPCQPSQLSQPAQPPSGKIPQVSQEAKGTQTGGVEQTRLPAIPTNRPSEP 2966
Cdd:PHA03247  2899 ALPPDQPERPPQPQAPPPPQPQPQ---PPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVP 2975
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2967 HAQL--QRAPVETAQPAHPSPVSVSMkPDLPSPLSSQA----------APKQPLFVPANSGPSTPPGLALPHAE------ 3028
Cdd:PHA03247  2976 RFRVpqPAPSREAPASSTPPLTGHSL-SRVSSWASSLAlheetdpppvSLKQTLWPPDDTEDSDADSLFDSDSErsdlea 3054
                          570
                   ....*....|....*...
gi 1907156703 3029 VQPAPKQESSPHGTPQRP 3046
Cdd:PHA03247  3055 LDPLPPEPHDPFAHEPDP 3072
PHA03247 super family cl33720
large tegument protein UL36; Provisional
1694-2214 5.91e-05

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 49.17  E-value: 5.91e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1694 EAGPAAASPqeSESPQKGSGSSPQLANNPADPDREAEEESASASTAPPEGTQLARQIElEQAVQNIAKLPEPSAAAASKG 1773
Cdd:PHA03247  2486 ARFPFAAGA--APDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLTWIRGLE-ELASDDAGDPPPPLPPAAPPA 2562
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1774 TATATAASEEPAPEHGhKPAHQASETELAA----AIGSIISDASGEPENFSAPPSVPPGSQTHPREGMEPGLHEAESGIL 1849
Cdd:PHA03247  2563 APDRSVPPPRPAPRPS-EPAVTSRARRPDAppqsARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPH 2641
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1850 ETGTATESSAPQVSAL--------------DPPEGSADTKETR--------GNSGDSVQ-EAKGSKVEVTPPRKDKGRQK 1906
Cdd:PHA03247  2642 PPPTVPPPERPRDDPApgrvsrprrarrlgRAAQASSPPQRPRrraarptvGSLTSLADpPPPPPTPEPAPHALVSATPL 2721
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1907 TTRRRKRNANKKVVAITETRASEAEQTQSESPAAEEATAATPEAPQEEKQSEKPPSPPAECTFDPSKTPPAESLSQENSA 1986
Cdd:PHA03247  2722 PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSP 2801
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1987 AEKTPCKAPVL---PALPPLSQPALMDDGPQArfkvhsiieSDPVTPPSDSGIPPPTIPLVTiAKLPPPVIPGGVPHQSP 2063
Cdd:PHA03247  2802 WDPADPPAAVLapaAALPPAASPAGPLPPPTS---------AQPTAPPPPPGPPPPSLPLGG-SVAPGGDVRRRPPSRSP 2871
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2064 PPKVTEwitrQEEPRAQSTPSPALPPDTKAsdmdtssstlrkiLMDPKYVSATGVTSTSVTSAIAEPVSAPCLQEAPAPP 2143
Cdd:PHA03247  2872 AAKPAA----PARPPVRRLARPAVSRSTES-------------FALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPP 2934
                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703 2144 CDPKHPPlegvsaAAVPNADTQASEVPVAADKEKVAPVIAPkitsviSRMPVSIDLENSQKITLAKPAPQT 2214
Cdd:PHA03247  2935 PPPRPQP------PLAPTTDPAGAGEPSGAVPQPWLGALVP------GRVAVPRFRVPQPAPSREAPASST 2993
Collagen_mid super family cl24528
Bacterial collagen, middle region; Collagen_mid is the conserved central region of bacterial ...
2213-2291 5.71e-04

Bacterial collagen, middle region; Collagen_mid is the conserved central region of bacterial collagen triple helix repeat proteins.


The actual alignment was detected with superfamily member pfam15984:

Pssm-ID: 435053 [Multi-domain]  Cd Length: 198  Bit Score: 43.86  E-value: 5.71e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2213 QTLTGLVSALTGLVNVSLVPVNALKGPVKGSVATLKGLVSTPAGPVN--LLKGPVNVLTGPVNVLTTPVSATVG----TV 2286
Cdd:pfam15984   60 NAVTSAGQLVSGLGTGPLAPLAPVTTPLGGTVSTLGGAVTGGGTTLGtaLSTGPVQQLTQQVSSAITPITSTVTgttqTV 139

                   ....*
gi 1907156703 2287 NAAPG 2291
Cdd:pfam15984  140 GAATG 144
 
Name Accession Description Interval E-value
SPOC_SHARP cd21543
SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor ...
3056-3216 1.66e-97

SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; SHARP, also called Msx2-interacting protein (MINT), or Spen homolog, is an estrogen-inducible transcriptional repressor that interacts directly with transcriptional corepressors silencing mediator for retinoid and thyroid receptor (SMRT)/nuclear receptor corepressor (NCoR), histone deacetylases (HDACs), and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also called RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain that binds to SMRT/NcoR. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439206  Cd Length: 163  Bit Score: 311.45  E-value: 1.66e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3056 KYPIVWQGLLALKNDTAAVQLHFVSGNNVLAHRSLPLSEGG---PPLRIAQRMRLEASQLEGVARRMTVETDYCLLLALP 3132
Cdd:cd21543      1 RYPVVWQGLLALKNDEAAVQMHYVSGNQDLAKRSLPRHLTNgnlPPLRIAQRMRLEPSQLEGVARKMQDESEYCLLLALP 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3133 CGRDQEDVVSQTESLKAAFITYLQAKQAAGIINVPNPGSNQPAYVLQIFPPCEFSESHLSRLAPDLLASISNIsPHLMIV 3212
Cdd:cd21543     81 CGRDQEDVLKQTNNLKNGFITYLQQKQAAGIVNVPNPGSQQPAYVVHIFPPCEFSNSHLSRLAPDLLNSIADI-PHLMIV 159

                   ....
gi 1907156703 3213 IASV 3216
Cdd:cd21543    160 IATV 163
RRM4_SHARP cd12351
RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
107-183 8.19e-47

RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409787 [Multi-domain]  Cd Length: 77  Bit Score: 162.93  E-value: 8.19e-47
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703  107 FGKSMPTNCVWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDF 183
Cdd:cd12351      1 FGKSMPTNCVWLDGLSENVTEQYLTRHFCRYGPVVKVVIDRQKGMALVLYDEVECAQAAVKETKGRKIGGRKIQVDF 77
RRM3_SHARP cd12350
RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
33-106 3.44e-45

RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409786 [Multi-domain]  Cd Length: 74  Bit Score: 158.34  E-value: 3.44e-45
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907156703   33 ATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLG 106
Cdd:cd12350      1 ATRTLFIGNLEKTTTYGDLRNIFERFGEIIDIDIKKQNGNPQYAFLQYCDIASVVKAIKKMDGEYLGNNRLKLG 74
SPOC pfam07744
SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in ...
3053-3216 2.08e-28

SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling.


Pssm-ID: 400205  Cd Length: 142  Bit Score: 112.83  E-value: 2.08e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3053 LKQKYPIVWQGLLALKN-DTAAVQLHFVSGNNVLAHRSLplseggppLRIAQRMRLEASQ--LEGVARRMTveTDYCLLL 3129
Cdd:pfam07744    1 SLQDLEVIWQGTLAMKGvAEFSVRAHLVSGDIDSLLPSL--------LRITGRIRLDAVWkyLDEVRRSIT--RDVLVVR 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3130 ALPCgrDQEDVVSQTEslkaaFITYLQAKQAAGIInvpNPGSNQpAYVLQIFPPCEFSESHLSRlapDLLASISNiSPHL 3209
Cdd:pfam07744   71 FFPS--SESDESAFDE-----LIDYLQSKQRAGVI---HAKSAD-VKDLYLFPPCEFLELLLPV---GLSLEVSE-PNLL 135

                   ....*..
gi 1907156703 3210 MIVIASV 3216
Cdd:pfam07744  136 LGVVVRK 142
RRM smart00360
RNA recognition motif;
36-105 7.03e-15

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 71.86  E-value: 7.03e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907156703    36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 105
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLvrDKETGKSKgFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
37-104 4.14e-12

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 63.79  E-value: 4.14e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLK 104
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLvRDETGRSKgFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM smart00360
RNA recognition motif;
115-181 1.23e-11

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 62.61  E-value: 1.23e-11
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907156703   115 CVWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD----RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 181
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKFGKVesVRLVRDketgKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
PHA03247 PHA03247
large tegument protein UL36; Provisional
1201-1635 1.62e-10

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 67.66  E-value: 1.62e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1201 PETHPKTPEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAgekPAEPAPVSEETKLVSEPASV 1280
Cdd:PHA03247  2571 PRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPP---PPSPSPAANEPDPHPPPTVP 2647
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1281 PVEQPRQSDVPPgedsRDSQDSAALAPSAPQESAATDAVPCVNAEPltpgTTVSQVESSVDPKP------SSPQPLSKLT 1354
Cdd:PHA03247  2648 PPERPRDDPAPG----RVSRPRRARRLGRAAQASSPPQRPRRRAAR----PTVGSLTSLADPPPppptpePAPHALVSAT 2719
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1355 QRSEEAEEGKVEKPDTTPSTEPDATQNAGVASEA-QPPASEDVEANPPVAAKDRKTNKSKRSKTSVQAAAASVVEKPVtr 1433
Cdd:PHA03247  2720 PLPPGPAAARQASPALPAAPAPPAVPAGPATPGGpARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRES-- 2797
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1434 kseridreklkrSSSPRGEAQKLLELKMEAEKITRTASKSSGGDTehPEPSLPLSRSRRRNVRSVYATMT-------DHE 1506
Cdd:PHA03247  2798 ------------LPSPWDPADPPAAVLAPAAALPPAASPAGPLPP--PTSAQPTAPPPPPGPPPPSLPLGgsvapggDVR 2863
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1507 SRSPAKEPVEQP---------RVTRKRLERELQEAVVPPTTPRRGRPPKTRRRAEEDGEHERKEPAETPRPAEGWRSPRS 1577
Cdd:PHA03247  2864 RRPPSRSPAAKPaaparppvrRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPL 2943
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907156703 1578 QKSAAAAGPQGKRGRNEQKVEAAAEAGAQASTREGNPKSRGEREAASEPKRDRRDPST 1635
Cdd:PHA03247  2944 APTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSL 3001
PTZ00121 PTZ00121
MAEBL; Provisional
213-844 8.81e-10

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 65.16  E-value: 8.81e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  213 RREERRGSYEY--SQERTYYENVRTPgtypEDSRRDYPARGREFYSEWETYQGEYYDSRYYDEPREYREYRSDPyEQDIR 290
Cdd:PTZ00121  1189 KAEELRKAEDArkAEAARKAEEERKA----EEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFE-EARMA 1263
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  291 EYSYRQRERERERERFESD--------------RDHERRPIERSQSPVHLRRPQSPGVSPAHSERLPSDSERRLYRRSSE 356
Cdd:PTZ00121  1264 HFARRQAAIKAEEARKADElkkaeekkkadeakKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKK 1343
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  357 RSGSCSSVSPPRYDKLEKARlerytKNEKADKERTfdpERVERERRIVRKEKGEKDKAERQKRKGKAHSPSSQPSETEQE 436
Cdd:PTZ00121  1344 AAEAAKAEAEAAADEAEAAE-----EKAEAAEKKK---EEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAA 1415
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  437 NDREQSPEKPRGSTKLSRDRADKEGPAKNRLELVpcvvltRVKEKEGKVIEHPPP---EKLKA-RLGRDTTKASALDQKP 512
Cdd:PTZ00121  1416 AKKKADEAKKKAEEKKKADEAKKKAEEAKKADEA------KKKAEEAKKAEEAKKkaeEAKKAdEAKKKAEEAKKADEAK 1489
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  513 QAAQGEPAKSDPARGKALREKVLPSHAEVGEKEGRTKLRKHLKAEQTPELSALDlEKLEARKRRFADSGLKIE-KQKPEI 591
Cdd:PTZ00121  1490 KKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAE-EKKKADELKKAEELKKAEeKKKAEE 1568
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  592 KKTSPETEDT---RILLKKQPDTSRDGVLLREGESERKPVRKEILKRESKKTKLERLNSALSPKDCQDPAAVSAGSGSRP 668
Cdd:PTZ00121  1569 AKKAEEDKNMalrKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKK 1648
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  669 SSDVHAglgelthgsvETQETQPKKAIPSKPQPKQLQLLENQGPEKEEVRKNYCRPREEPAEHRAGQEKPHGGNAEEKLG 748
Cdd:PTZ00121  1649 AEELKK----------AEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKA 1718
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  749 IDIDHTQSYRK-QMEQSRRKQrmEMEIAKAEKFgspkkDVDDYERRSLVHEVGKPPQDVTDDSPPSKKRRTDHVDFDICT 827
Cdd:PTZ00121  1719 EELKKAEEENKiKAEEAKKEA--EEDKKKAEEA-----KKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEK 1791
                          650
                   ....*....|....*..
gi 1907156703  828 KRERNYRSSRQISEDSE 844
Cdd:PTZ00121  1792 RRMEVDKKIKDIFDNFA 1808
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
19-189 5.29e-09

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 61.75  E-value: 5.29e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   19 FRPLDERIDEFHPKATrTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK--VNGVPQYAFLQYCDIASVCKAIKKMDGE 96
Cdd:TIGR01628  164 FIKKHEREAAPLKKFT-NLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKdgSGRSRGFAFVNFEKHEDAAKAVEEMNGK 242
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   97 YLGN----NRLKLG-----------------------FGKSMPTNcVWLDGLSSNVSDQYLTRHFCRYGPVV--KVVFD- 146
Cdd:TIGR01628  243 KIGLakegKKLYVGraqkraereaelrrkfeelqqerKMKAQGVN-LYVKNLDDTVTDEKLRELFSECGEITsaKVMLDe 321
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 1907156703  147 --RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANRESQ 189
Cdd:TIGR01628  322 kgVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQ 366
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
37-178 2.06e-08

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 59.82  E-value: 2.06e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLgfGKSMP-- 112
Cdd:TIGR01628   91 IFVKNLDKSVDNKALFDTFSKFGNILSCKVaTDENGKSRgYGFVHFEKEESAKAAIQKVNGMLLNDKEVYV--GRFIKkh 168
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  113 ----------TNcVWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRL-----KGMALVLYSEIEDAQAAVKETKGRKIGGN 177
Cdd:TIGR01628  169 ereaaplkkfTN-LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDgsgrsRGFAFVNFEKHEDAAKAVEEMNGKKIGLA 247

                   .
gi 1907156703  178 K 178
Cdd:TIGR01628  248 K 248
PHA03247 PHA03247
large tegument protein UL36; Provisional
2521-3046 1.14e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 58.41  E-value: 1.14e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2521 PANLGPTLTPHHPPALP------------SKLPAEVNHVPSGPSTPADRTIAHLATPKPDTHSPRPTGPT-------PGL 2581
Cdd:PHA03247  2512 PSRLAPAILPDEPVGEPvhprmltwirglEELASDDAGDPPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAvtsrarrPDA 2591
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2582 FPRPCHPSSTTSTALSTNATVMLAAGIPVPqfissiHPEQSVIMPPHSITQTVSLGHLSQGEVRMSTPTLPSITYSIRPE 2661
Cdd:PHA03247  2592 PPQSARPRAPVDDRGDPRGPAPPSPLPPDT------HAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPR 2665
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2662 TLHSPRAPLQPQQiEARAPQRVGTPqPATTGVPALATQHPPEEEVHyhlPVARAAAPVQSEVLVMQSEYRLHPYT----- 2736
Cdd:PHA03247  2666 RARRLGRAAQASS-PPQRPRRRAAR-PTVGSLTSLADPPPPPPTPE---PAPHALVSATPLPPGPAAARQASPALpaapa 2740
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2737 ---------VPRDVRIMVHPHVTAVSEQPRATEGVVKVPPANKAPQQLVKEAVKTSDAKAVPAPAPVPVPVPVPTPAPPP 2807
Cdd:PHA03247  2741 ppavpagpaTPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPP 2820
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2808 HGEARILTVTPSSQLQGLPLTPPVVVTHGVQIVHSSGELFQEYRYGDVRTyhAPAQQLTHTQFPVASSISLA-SRTKTSA 2886
Cdd:PHA03247  2821 AASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRS--PAAKPAAPARPPVRRLARPAvSRSTESF 2898
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2887 QVPPEGEPLQSTQSAQPAPSTQATqpiPPAPPCQPSQLSQPAQPPSGKIPQVSQEAKGTQTGGVEQTRLPAIPTNRPSEP 2966
Cdd:PHA03247  2899 ALPPDQPERPPQPQAPPPPQPQPQ---PPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVP 2975
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2967 HAQL--QRAPVETAQPAHPSPVSVSMkPDLPSPLSSQA----------APKQPLFVPANSGPSTPPGLALPHAE------ 3028
Cdd:PHA03247  2976 RFRVpqPAPSREAPASSTPPLTGHSL-SRVSSWASSLAlheetdpppvSLKQTLWPPDDTEDSDADSLFDSDSErsdlea 3054
                          570
                   ....*....|....*...
gi 1907156703 3029 VQPAPKQESSPHGTPQRP 3046
Cdd:PHA03247  3055 LDPLPPEPHDPFAHEPDP 3072
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
116-180 4.28e-07

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 49.54  E-value: 4.28e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD---RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIK 180
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIksIRLVRDetgRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
sex-lethal TIGR01659
sex-lethal family splicing factor; This model describes the sex-lethal family of splicing ...
27-166 8.67e-06

sex-lethal family splicing factor; This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).


Pssm-ID: 273740 [Multi-domain]  Cd Length: 346  Bit Score: 50.79  E-value: 8.67e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   27 DEFHPKATRTLFIGN-LEKTTTYHDLRNIFQRFGEIVDIDIK---KVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNR 102
Cdd:TIGR01659   99 DDNDTNNSGTNLIVNyLPQDMTDRELYALFRTIGPINTCRIMrdyKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKR 178
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907156703  103 LKLGF----GKSMPTNCVWLDGLSSNVSDQYLTRHFCRYGPVVK--VVFDRL----KGMALVLYSEIEDAQAAV 166
Cdd:TIGR01659  179 LKVSYarpgGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQknILRDKLtgtpRGVAFVRFNKREEAQEAI 252
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
34-104 1.09e-05

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 45.86  E-value: 1.09e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907156703   34 TRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIK--KVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLK 104
Cdd:COG0724      1 SMKIYVGNLPYSVTEEDLRELFSEYGEVTSVKLItdRETGRSRgFGFVEMPDDEEAQAAIEALNGAELMGRTLK 74
PHA03247 PHA03247
large tegument protein UL36; Provisional
1694-2214 5.91e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 49.17  E-value: 5.91e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1694 EAGPAAASPqeSESPQKGSGSSPQLANNPADPDREAEEESASASTAPPEGTQLARQIElEQAVQNIAKLPEPSAAAASKG 1773
Cdd:PHA03247  2486 ARFPFAAGA--APDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLTWIRGLE-ELASDDAGDPPPPLPPAAPPA 2562
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1774 TATATAASEEPAPEHGhKPAHQASETELAA----AIGSIISDASGEPENFSAPPSVPPGSQTHPREGMEPGLHEAESGIL 1849
Cdd:PHA03247  2563 APDRSVPPPRPAPRPS-EPAVTSRARRPDAppqsARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPH 2641
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1850 ETGTATESSAPQVSAL--------------DPPEGSADTKETR--------GNSGDSVQ-EAKGSKVEVTPPRKDKGRQK 1906
Cdd:PHA03247  2642 PPPTVPPPERPRDDPApgrvsrprrarrlgRAAQASSPPQRPRrraarptvGSLTSLADpPPPPPTPEPAPHALVSATPL 2721
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1907 TTRRRKRNANKKVVAITETRASEAEQTQSESPAAEEATAATPEAPQEEKQSEKPPSPPAECTFDPSKTPPAESLSQENSA 1986
Cdd:PHA03247  2722 PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSP 2801
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1987 AEKTPCKAPVL---PALPPLSQPALMDDGPQArfkvhsiieSDPVTPPSDSGIPPPTIPLVTiAKLPPPVIPGGVPHQSP 2063
Cdd:PHA03247  2802 WDPADPPAAVLapaAALPPAASPAGPLPPPTS---------AQPTAPPPPPGPPPPSLPLGG-SVAPGGDVRRRPPSRSP 2871
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2064 PPKVTEwitrQEEPRAQSTPSPALPPDTKAsdmdtssstlrkiLMDPKYVSATGVTSTSVTSAIAEPVSAPCLQEAPAPP 2143
Cdd:PHA03247  2872 AAKPAA----PARPPVRRLARPAVSRSTES-------------FALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPP 2934
                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703 2144 CDPKHPPlegvsaAAVPNADTQASEVPVAADKEKVAPVIAPkitsviSRMPVSIDLENSQKITLAKPAPQT 2214
Cdd:PHA03247  2935 PPPRPQP------PLAPTTDPAGAGEPSGAVPQPWLGALVP------GRVAVPRFRVPQPAPSREAPASST 2993
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
105-188 7.49e-05

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 45.41  E-value: 7.49e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  105 LGFGKSMPTNcVWLDGLSSNVSDQYLTRHFCRYGPVV--KVVFDR----LKGMALVLYSEIEDAQAAVKETKGRKIGGNK 178
Cdd:PLN03134    27 LGSLRLMSTK-LFIGGLSWGTDDASLRDAFAHFGDVVdaKVIVDRetgrSRGFGFVNFNDEGAATAAISEMDGKELNGRH 105
                           90
                   ....*....|
gi 1907156703  179 IKVDFANRES 188
Cdd:PLN03134   106 IRVNPANDRP 115
Collagen_mid pfam15984
Bacterial collagen, middle region; Collagen_mid is the conserved central region of bacterial ...
2213-2291 5.71e-04

Bacterial collagen, middle region; Collagen_mid is the conserved central region of bacterial collagen triple helix repeat proteins.


Pssm-ID: 435053 [Multi-domain]  Cd Length: 198  Bit Score: 43.86  E-value: 5.71e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2213 QTLTGLVSALTGLVNVSLVPVNALKGPVKGSVATLKGLVSTPAGPVN--LLKGPVNVLTGPVNVLTTPVSATVG----TV 2286
Cdd:pfam15984   60 NAVTSAGQLVSGLGTGPLAPLAPVTTPLGGTVSTLGGAVTGGGTTLGtaLSTGPVQQLTQQVSSAITPITSTVTgttqTV 139

                   ....*
gi 1907156703 2287 NAAPG 2291
Cdd:pfam15984  140 GAATG 144
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
2860-3052 6.48e-04

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 45.41  E-value: 6.48e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2860 APAQQLTHTQFPVASSISLASRTKTSAQvppEGEPLQSTQSAQPAPSTQATQPIPPAPPCQPSQLSQPAQPPSGKIPQVS 2939
Cdd:pfam09770  170 AAAPAPAPQPAAQPASLPAPSRKMMSLE---EVEAAMRAQAKKPAQQPAPAPAQPPAAPPAQQAQQQQQFPPQIQQQQQP 246
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2940 QEAKGtqtggveqtrlPAIPTNRPSEPHAQLQRAPVETAQPAHPSPVSVSmKPDLPSPLSSQAAPKQPL-----FVPANS 3014
Cdd:pfam09770  247 QQQPQ-----------QPQQHPGQGHPVTILQRPQSPQPDPAQPSIQPQA-QQFHQQPPPVPVQPTQILqnpnrLSAARV 314
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 1907156703 3015 GPSTPPGLALPHAEVQPAPKQESSPHGTPQ---RPVDMVQL 3052
Cdd:pfam09770  315 GYPQNPQPGVQPAPAHQAHRQQGSFGRQAPiitHPQQLAQL 355
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
37-113 2.14e-03

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 41.18  E-value: 2.14e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGKSMPT 113
Cdd:PLN03134    37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVivdRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPS 116
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
1508-1775 9.74e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 41.79  E-value: 9.74e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1508 RSPAKEPVEQPRVTRKRlerelQEAVVPPTTPRRGRPPKTRRRAEedgeherkePAETPRPAEGWRSPRSQKSAAAAGPQ 1587
Cdd:PRK12323   375 ATAAAAPVAQPAPAAAA-----PAAAAPAPAAPPAAPAAAPAAAA---------AARAVAAAPARRSPAPEALAAARQAS 440
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1588 GKRGRNEQKVEAAAEAGAQASTREGNPKSRGEREAASEPKRDRRDPSTDKNGPDTFPveVLERKPPEKtykskrgrARST 1667
Cdd:PRK12323   441 ARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPP--PWEELPPEF--------ASPA 510
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1668 RSAMDRAAHQRSLEMAARAAGQAADKEAGPAAASPQESESPQKGSGSSPQLANNPADPDREAEEESASAS------TAPP 1741
Cdd:PRK12323   511 PAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVVAPRPPRASASGLPDMFDGDwpalaaRLPV 590
                          250       260       270
                   ....*....|....*....|....*....|....*.
gi 1907156703 1742 EG--TQLARQIELEQAVQNIAKLPEPSAAAASKGTA 1775
Cdd:PRK12323   591 RGlaQQLARQSELAGVEGDTVRLRVPVPALAEAEVV 626
 
Name Accession Description Interval E-value
SPOC_SHARP cd21543
SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor ...
3056-3216 1.66e-97

SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; SHARP, also called Msx2-interacting protein (MINT), or Spen homolog, is an estrogen-inducible transcriptional repressor that interacts directly with transcriptional corepressors silencing mediator for retinoid and thyroid receptor (SMRT)/nuclear receptor corepressor (NCoR), histone deacetylases (HDACs), and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also called RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain that binds to SMRT/NcoR. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439206  Cd Length: 163  Bit Score: 311.45  E-value: 1.66e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3056 KYPIVWQGLLALKNDTAAVQLHFVSGNNVLAHRSLPLSEGG---PPLRIAQRMRLEASQLEGVARRMTVETDYCLLLALP 3132
Cdd:cd21543      1 RYPVVWQGLLALKNDEAAVQMHYVSGNQDLAKRSLPRHLTNgnlPPLRIAQRMRLEPSQLEGVARKMQDESEYCLLLALP 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3133 CGRDQEDVVSQTESLKAAFITYLQAKQAAGIINVPNPGSNQPAYVLQIFPPCEFSESHLSRLAPDLLASISNIsPHLMIV 3212
Cdd:cd21543     81 CGRDQEDVLKQTNNLKNGFITYLQQKQAAGIVNVPNPGSQQPAYVVHIFPPCEFSNSHLSRLAPDLLNSIADI-PHLMIV 159

                   ....
gi 1907156703 3213 IASV 3216
Cdd:cd21543    160 IATV 163
SPOC_SF cd21520
SPOC (Spen paralog and ortholog C-terminal) domain superfamily; The SPOC domain is involved in ...
3060-3214 3.15e-52

SPOC (Spen paralog and ortholog C-terminal) domain superfamily; The SPOC domain is involved in developmental signalling and has also been proposed to be a phosphorylation binding module. It has been found mainly in two protein families: transcription factor S-II (TFIIS) and Spen (split end). The TFIIS family includes SPOC domain-containing protein 1 (SPOCD1), yeast bypass of ESS1 protein 1 (Bye1p), PHD finger protein 3 (PHF3), and death-inducer obliterator (Dido) splicing variants, among others. They are characterized by having both a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal SPOC domain. The Spen protein family includes SMART/HDAC1-associated repressor protein (SHARP) and RNA binding motif protein 15 (RBM15)-like proteins from metazoans, as well as plant flowering time control protein FPA and yeast chromo domain-containing protein 1 (Chp1p). They are characterized by containing RNA recognition motifs (RRMs) and a SPOC domain.


Pssm-ID: 439200  Cd Length: 138  Bit Score: 180.95  E-value: 3.15e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3060 VWQGLLALKND-TAAVQLHFVSGNNVLAhrslpLSEGGPPLRIAQRMRLEASQLEGVARRMTVETDYCLLLALPCGRDQe 3138
Cdd:cd21520      1 VWQGLLALKNDpTAAARLHFVSGNNVLA-----LSELPPVLRIAQRMRLNATQLEGVARRMAVATDYCLVLALPCGRDD- 74
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907156703 3139 dvvsqtESLKAAFITYLQAKQAAGIInvpnpgSNQPAYVLQIFPPCEFSESHLSRLAPDLLASISNISPHLMIVIA 3214
Cdd:cd21520     75 ------ESLKAAFITYLQAKQRAGIA------SNQPAYVLQLFPPCEFSESHLSRLAPDLLASIVTISPHLMIVIL 138
SPOC_Spen cd21539
SPOC (Spen paralog and ortholog C-terminal) domain found in the Spen (split end) protein ...
3060-3214 1.26e-49

SPOC (Spen paralog and ortholog C-terminal) domain found in the Spen (split end) protein family; The Spen protein family includes a group of proteins characterized by containing RNA recognition motifs (RRMs) and a SPOC domain, such as SMART/HDAC1-associated repressor protein (SHARP) and RNA binding motif protein 15 (RBM15)-like proteins from metazoans, as well as plant flowering time control protein FPA and yeast chromo domain-containing protein 1 (Chp1p). SHARP, also called Msx2-interacting protein (MINT), or Spen homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs), and components of the NuRD complex. RBM15, also called one-twenty two protein 1 (OTT1), is a novel mRNA export factor and component of the NXF1 pathway. RNA-binding protein 15B (RBM15B), also called one-twenty two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. Chp1p is a component of the kinetochore which plays a role in stabilizing microtubules and thus, allowing accurate chromosome segregation. It has a role in the RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation. FPA plays a role in the regulation of flowering time in the autonomous flowering pathway by decreasing FLOWERING LOCUS C mRNA levels. It is required for RNA-mediated chromatin silencing of a range of loci in the genome. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439202  Cd Length: 148  Bit Score: 173.84  E-value: 1.26e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3060 VWQGLLALKNDTAAVQLHFVSGNNVLAH-RSLPLSEGGPPLRIAQRMRLEASQLEGvaRRMTVETDYCLLLALPCGRDQE 3138
Cdd:cd21539      1 IWRGVLLVKNSAFLFRCHLAKGDAEIASqQLLRETVSCPQVDIVQRMRLDELALFE--RSGAVATGLAILLALPCGDDSI 78
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907156703 3139 DVVSQTESLKAAFITYLQAKQAAGIINVPNPgsnQPAYVLQIFPPCEFSESHLSRLapdLLASISNISPHLMIVIA 3214
Cdd:cd21539     79 SSASITEAPLTNFVSYLKAKQAAGVVLLSDD---HENYVLLLFPPSEFSLSLLKRS---LNSEQATSDSYLVMVVV 148
RRM4_SHARP cd12351
RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
107-183 8.19e-47

RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409787 [Multi-domain]  Cd Length: 77  Bit Score: 162.93  E-value: 8.19e-47
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703  107 FGKSMPTNCVWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDF 183
Cdd:cd12351      1 FGKSMPTNCVWLDGLSENVTEQYLTRHFCRYGPVVKVVIDRQKGMALVLYDEVECAQAAVKETKGRKIGGRKIQVDF 77
RRM3_SHARP cd12350
RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
33-106 3.44e-45

RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409786 [Multi-domain]  Cd Length: 74  Bit Score: 158.34  E-value: 3.44e-45
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907156703   33 ATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLG 106
Cdd:cd12350      1 ATRTLFIGNLEKTTTYGDLRNIFERFGEIIDIDIKKQNGNPQYAFLQYCDIASVVKAIKKMDGEYLGNNRLKLG 74
SPOC_RBM15-like cd21544
SPOC (Spen paralog and ortholog C-terminal) domain found in RNA binding motif protein 15 ...
3060-3213 5.40e-32

SPOC (Spen paralog and ortholog C-terminal) domain found in RNA binding motif protein 15 (RBM15) and similar proteins; This subfamily includes RBM15, RBM15B, and similar proteins found in metazoans. RBM15, also called one-twenty two protein 1 (OTT1), is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as a receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also called one-twenty two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein that shares with RBM15, the association with the splicing factor compartment and the nuclear envelope, as well as the binding to mRNA export factors NXF1 and Aly/REF. Members of this family have a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439207  Cd Length: 164  Bit Score: 123.93  E-value: 5.40e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3060 VWQGLLALKNDTAAVQLHFVSGNNVLA--HRSLPLSEGGPPLRIAQRMRLEASQLEGVARRMTVETD--YCLLLALP--C 3133
Cdd:cd21544      1 VWSGALVLKNSAFPVRMHLLRGDVQLAdtLLPNPTSGEQPVLRITQRLRLDPPKLDDVSRRISSAGSsgYCVLLAVPgsG 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3134 GRDQEDVVSQTESLKaAFITYLQAKQAAGIINVPNPGSNQP---AYVLQIFPPCEFSESHLSRLAPDLLASISNISpHLM 3210
Cdd:cd21544     81 ANSEADASTQQRPLR-NLVSYLKQKEAAGVVSLPPNGSVGEkkvTGVLHAFPPCDFSQQLLRRLAPSLSLESLKDD-HLV 158

                   ...
gi 1907156703 3211 IVI 3213
Cdd:cd21544    159 IVL 161
SPOC pfam07744
SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in ...
3053-3216 2.08e-28

SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling.


Pssm-ID: 400205  Cd Length: 142  Bit Score: 112.83  E-value: 2.08e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3053 LKQKYPIVWQGLLALKN-DTAAVQLHFVSGNNVLAHRSLplseggppLRIAQRMRLEASQ--LEGVARRMTveTDYCLLL 3129
Cdd:pfam07744    1 SLQDLEVIWQGTLAMKGvAEFSVRAHLVSGDIDSLLPSL--------LRITGRIRLDAVWkyLDEVRRSIT--RDVLVVR 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3130 ALPCgrDQEDVVSQTEslkaaFITYLQAKQAAGIInvpNPGSNQpAYVLQIFPPCEFSESHLSRlapDLLASISNiSPHL 3209
Cdd:pfam07744   71 FFPS--SESDESAFDE-----LIDYLQSKQRAGVI---HAKSAD-VKDLYLFPPCEFLELLLPV---GLSLEVSE-PNLL 135

                   ....*..
gi 1907156703 3210 MIVIASV 3216
Cdd:pfam07744  136 LGVVVRK 142
SPOC_RBM15 cd21549
SPOC (Spen paralog and ortholog C-terminal) domain found in vertebrate RNA binding motif ...
3061-3201 1.01e-20

SPOC (Spen paralog and ortholog C-terminal) domain found in vertebrate RNA binding motif protein 15 (RBM15); RBM15, also called one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439212  Cd Length: 164  Bit Score: 91.49  E-value: 1.01e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3061 WQGLLALKNDTAAVQLHFVSGNNVLAHRSL-PLSEGG--PPLRIAQRMRLEASQLEGVARRMTVE--TDYCLLLALPCGR 3135
Cdd:cd21549      2 WQGMLLLKNSNFPSNMHLLEGDLSVASSLLvDGSTGGkvAQLKITQRLRLDQPKLDEVTRRIKVAgpNGYAVLLAVPGSS 81
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703 3136 DQEDVVSQTESLKAAF---ITYLQAKQAAGIINVPNPGSNQP--AYVLQIFPPCEFSESHLSRLAPDLLAS 3201
Cdd:cd21549     82 EVSSVSDQATSTQRPLrnlVSYLKQKQAAGVISLPVGGSKDKdnTGVLHAFPPCDFSQQFLDSSAKALAKS 152
RRM2_Spen cd12309
RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily ...
33-109 7.36e-18

RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 240755 [Multi-domain]  Cd Length: 79  Bit Score: 80.52  E-value: 7.36e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703   33 ATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKV--NGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 109
Cdd:cd12309      1 ATRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPprGQGNAYAFVKFLNLDMAHRAKVAMSGQYIGRNQIKIGYGK 79
RRM smart00360
RNA recognition motif;
36-105 7.03e-15

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 71.86  E-value: 7.03e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907156703    36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 105
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLvrDKETGKSKgFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
37-105 9.59e-15

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 71.16  E-value: 9.59e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 105
Cdd:cd00590      1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIvRDRDGKSKgFAFVEFESPEDAEKALEALNGTELGGRPLKV 71
RRM2_RBM15 cd12555
RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
32-112 2.26e-14

RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.


Pssm-ID: 409971 [Multi-domain]  Cd Length: 87  Bit Score: 70.65  E-value: 2.26e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   32 KATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVN--GVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 109
Cdd:cd12555      5 RANRTLFLGNLDITVTENDLRRAFDRFGVITEVDIKRPGrgQTSTYGFLKFENLDMAHRAKLAMSGKVIGRNPIKIGYGK 84

                   ...
gi 1907156703  110 SMP 112
Cdd:cd12555     85 ATP 87
SPOC_RBM15B cd21550
SPOC (Spen paralog and ortholog C-terminal) domain found in putative RNA binding motif protein ...
3060-3213 5.20e-14

SPOC (Spen paralog and ortholog C-terminal) domain found in putative RNA binding motif protein 15B (RBM15B); RBM15B, also called one-twenty two 3 (OTT3), is a paralog of RNA binding motif protein 15 (RBM15), which is also known as one-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein that shares with RBM15, the association with the splicing factor compartment and the nuclear envelope, as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which contains a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439213  Cd Length: 167  Bit Score: 72.58  E-value: 5.20e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3060 VWQGLLALKNDTAAVQLHFVSGNNVLAHRSLP-LSEGG--PPLRIAQRMRLEASQLEGVARRMTVET--DYCLLLAL--- 3131
Cdd:cd21550      1 AWNGVLVLKNSCFPTNMHILEGDLGVVNILLKdYTSGGklTQLKIAQRLRLDQPKLDEVTRRIKQGSpdGYAVLLATqap 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3132 PCGRDQEDVVSQ---TESLKAAFITYLQAKQAAGIINVPNPGSNQ--PAYVLQIFPPCEFSESHLsRLAPDLLASISniS 3206
Cdd:cd21550     81 QGGEGGGAPPVEpglQRRLLRNLVSYLKQKQAAGVISLPVGGSKDrdNTGMLYAFPPCDFSQQYL-QSALRTLGKLE--E 157

                   ....*..
gi 1907156703 3207 PHLMIVI 3213
Cdd:cd21550    158 EHMVIVI 164
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
116-182 6.30e-13

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 66.15  E-value: 6.30e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVF-----DRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVD 182
Cdd:cd00590      1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIvrdrdGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
37-104 4.14e-12

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 63.79  E-value: 4.14e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLK 104
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLvRDETGRSKgFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM smart00360
RNA recognition motif;
115-181 1.23e-11

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 62.61  E-value: 1.23e-11
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907156703   115 CVWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD----RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 181
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKFGKVesVRLVRDketgKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
PHA03247 PHA03247
large tegument protein UL36; Provisional
1201-1635 1.62e-10

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 67.66  E-value: 1.62e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1201 PETHPKTPEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAgekPAEPAPVSEETKLVSEPASV 1280
Cdd:PHA03247  2571 PRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPP---PPSPSPAANEPDPHPPPTVP 2647
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1281 PVEQPRQSDVPPgedsRDSQDSAALAPSAPQESAATDAVPCVNAEPltpgTTVSQVESSVDPKP------SSPQPLSKLT 1354
Cdd:PHA03247  2648 PPERPRDDPAPG----RVSRPRRARRLGRAAQASSPPQRPRRRAAR----PTVGSLTSLADPPPppptpePAPHALVSAT 2719
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1355 QRSEEAEEGKVEKPDTTPSTEPDATQNAGVASEA-QPPASEDVEANPPVAAKDRKTNKSKRSKTSVQAAAASVVEKPVtr 1433
Cdd:PHA03247  2720 PLPPGPAAARQASPALPAAPAPPAVPAGPATPGGpARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRES-- 2797
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1434 kseridreklkrSSSPRGEAQKLLELKMEAEKITRTASKSSGGDTehPEPSLPLSRSRRRNVRSVYATMT-------DHE 1506
Cdd:PHA03247  2798 ------------LPSPWDPADPPAAVLAPAAALPPAASPAGPLPP--PTSAQPTAPPPPPGPPPPSLPLGgsvapggDVR 2863
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1507 SRSPAKEPVEQP---------RVTRKRLERELQEAVVPPTTPRRGRPPKTRRRAEEDGEHERKEPAETPRPAEGWRSPRS 1577
Cdd:PHA03247  2864 RRPPSRSPAAKPaaparppvrRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPL 2943
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907156703 1578 QKSAAAAGPQGKRGRNEQKVEAAAEAGAQASTREGNPKSRGEREAASEPKRDRRDPST 1635
Cdd:PHA03247  2944 APTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSL 3001
RRM2_RBM15B cd12556
RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from ...
32-109 2.63e-10

RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from vertebrate; This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409972 [Multi-domain]  Cd Length: 85  Bit Score: 59.16  E-value: 2.63e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   32 KATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKvNGVPQ---YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFG 108
Cdd:cd12556      6 RATRNLFIGNLDHNVSEVELRRAFEKYGIIEEVVIKR-PARGQggaYAFLKFQNLDMAHRAKVAMSGRVIGRNPIKIGYG 84

                   .
gi 1907156703  109 K 109
Cdd:cd12556     85 K 85
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
36-108 3.75e-10

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 58.10  E-value: 3.75e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVpqyAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFG 108
Cdd:cd12346      3 TVFVGGLDPNVTEEDLRVLFGPFGEIVYVKIPPGKGC---GFVQFVNRASAEAAIQKLQGTPIGGSRIRLSWG 72
PTZ00121 PTZ00121
MAEBL; Provisional
213-844 8.81e-10

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 65.16  E-value: 8.81e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  213 RREERRGSYEY--SQERTYYENVRTPgtypEDSRRDYPARGREFYSEWETYQGEYYDSRYYDEPREYREYRSDPyEQDIR 290
Cdd:PTZ00121  1189 KAEELRKAEDArkAEAARKAEEERKA----EEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFE-EARMA 1263
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  291 EYSYRQRERERERERFESD--------------RDHERRPIERSQSPVHLRRPQSPGVSPAHSERLPSDSERRLYRRSSE 356
Cdd:PTZ00121  1264 HFARRQAAIKAEEARKADElkkaeekkkadeakKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKK 1343
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  357 RSGSCSSVSPPRYDKLEKARlerytKNEKADKERTfdpERVERERRIVRKEKGEKDKAERQKRKGKAHSPSSQPSETEQE 436
Cdd:PTZ00121  1344 AAEAAKAEAEAAADEAEAAE-----EKAEAAEKKK---EEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAA 1415
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  437 NDREQSPEKPRGSTKLSRDRADKEGPAKNRLELVpcvvltRVKEKEGKVIEHPPP---EKLKA-RLGRDTTKASALDQKP 512
Cdd:PTZ00121  1416 AKKKADEAKKKAEEKKKADEAKKKAEEAKKADEA------KKKAEEAKKAEEAKKkaeEAKKAdEAKKKAEEAKKADEAK 1489
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  513 QAAQGEPAKSDPARGKALREKVLPSHAEVGEKEGRTKLRKHLKAEQTPELSALDlEKLEARKRRFADSGLKIE-KQKPEI 591
Cdd:PTZ00121  1490 KKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAE-EKKKADELKKAEELKKAEeKKKAEE 1568
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  592 KKTSPETEDT---RILLKKQPDTSRDGVLLREGESERKPVRKEILKRESKKTKLERLNSALSPKDCQDPAAVSAGSGSRP 668
Cdd:PTZ00121  1569 AKKAEEDKNMalrKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKK 1648
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  669 SSDVHAglgelthgsvETQETQPKKAIPSKPQPKQLQLLENQGPEKEEVRKNYCRPREEPAEHRAGQEKPHGGNAEEKLG 748
Cdd:PTZ00121  1649 AEELKK----------AEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKA 1718
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  749 IDIDHTQSYRK-QMEQSRRKQrmEMEIAKAEKFgspkkDVDDYERRSLVHEVGKPPQDVTDDSPPSKKRRTDHVDFDICT 827
Cdd:PTZ00121  1719 EELKKAEEENKiKAEEAKKEA--EEDKKKAEEA-----KKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEK 1791
                          650
                   ....*....|....*..
gi 1907156703  828 KRERNYRSSRQISEDSE 844
Cdd:PTZ00121  1792 RRMEVDKKIKDIFDNFA 1808
RRM_TRA2 cd12363
RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and ...
113-184 1.27e-09

RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 409798 [Multi-domain]  Cd Length: 80  Bit Score: 56.85  E-value: 1.27e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907156703  113 TNCVWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD----RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12363      1 SRCLGVFGLSLYTTERDLREVFSRYGPIekVQVVYDqqtgRSRGFGFVYFESVEDAKEAKERLNGQEIDGRRIRVDYS 78
RRM_CIRBP_RBM3 cd12449
RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding ...
120-184 3.17e-09

RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain.


Pssm-ID: 409883 [Multi-domain]  Cd Length: 80  Bit Score: 55.95  E-value: 3.17e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703  120 GLSSNVSDQYLTRHFCRYGPVVKVVF------DRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12449      7 GLSFDTNEQSLEEVFSKYGQISEVVVvkdretQRSRGFGFVTFENPDDAKDAMMAMNGKSLDGRQIRVDQA 77
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
19-189 5.29e-09

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 61.75  E-value: 5.29e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   19 FRPLDERIDEFHPKATrTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK--VNGVPQYAFLQYCDIASVCKAIKKMDGE 96
Cdd:TIGR01628  164 FIKKHEREAAPLKKFT-NLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKdgSGRSRGFAFVNFEKHEDAAKAVEEMNGK 242
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   97 YLGN----NRLKLG-----------------------FGKSMPTNcVWLDGLSSNVSDQYLTRHFCRYGPVV--KVVFD- 146
Cdd:TIGR01628  243 KIGLakegKKLYVGraqkraereaelrrkfeelqqerKMKAQGVN-LYVKNLDDTVTDEKLRELFSECGEITsaKVMLDe 321
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 1907156703  147 --RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANRESQ 189
Cdd:TIGR01628  322 kgVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQ 366
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
114-184 7.36e-09

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 54.83  E-value: 7.36e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703  114 NCVWLDGLSSNVSDQYLTRHFCRYGPVV--KVVFDR----LKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12398      1 RSVFVGNIPYDATEEQLKEIFSEVGPVVsfRLVTDRetgkPKGYGFCEFRDAETALSAVRNLNGYELNGRPLRVDFA 77
RRM1_SRSF1_like cd12338
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
36-107 8.73e-09

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues.


Pssm-ID: 409775 [Multi-domain]  Cd Length: 72  Bit Score: 54.29  E-value: 8.73e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF 107
Cdd:cd12338      1 RIYVGNLPGDIRERDIEDLFYKYGPILAIDLKNRRRGPPFAFVEFEDPRDAEDAIRGRDGYDFDGYRLRVEF 72
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
116-184 1.07e-08

RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409881 [Multi-domain]  Cd Length: 76  Bit Score: 54.36  E-value: 1.07e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYGPVV--KVVFDRL----KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12447      2 LFVGGLSWNVDDPWLKKEFEKYGGVIsaRVITDRGsgrsKGYGYVDFATPEAAQKALAAMSGKEIDGRQINVDFS 76
PTZ00121 PTZ00121
MAEBL; Provisional
241-892 1.32e-08

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 61.31  E-value: 1.32e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  241 EDSRRDYPAR-GREFYSEWETYQGEyyDSRYYDEPREYREYRSdpyEQDIREYSYRQRERERERERFESDRDHERRPIER 319
Cdd:PTZ00121  1173 EDAKKAEAARkAEEVRKAEELRKAE--DARKAEAARKAEEERK---AEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEE 1247
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  320 SQSPVHLRRPQSPGVSPAHSERLPSDSERRLYRRSSERSGSCSSVSPPRYDKLEKARLERYTKNEKADK-ERTFDPERVE 398
Cdd:PTZ00121  1248 ERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKaDEAKKKAEEA 1327
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  399 RERRIVRKEKGE--KDKAERQKRKGKAHSPSSQPSETEQENDREQSPEKPRGSTKLSR--DRADKEGPAKNRLELVPcvv 474
Cdd:PTZ00121  1328 KKKADAAKKKAEeaKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKkaEEKKKADEAKKKAEEDK--- 1404
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  475 lTRVKEKEGKVIEHPPPEKLKARlGRDTTKASALDQKPQaaqgEPAKSDPARGKAlREKVLPSHAEVGEKEGRTKLRKHL 554
Cdd:PTZ00121  1405 -KKADELKKAAAAKKKADEAKKK-AEEKKKADEAKKKAE----EAKKADEAKKKA-EEAKKAEEAKKKAEEAKKADEAKK 1477
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  555 KAEQTPELSALDLEKLEARKRrfADSGLKIEKQKPEIKKTSPETEDTRILLKKQPDTSRDGVLLREGESERKP--VRK-E 631
Cdd:PTZ00121  1478 KAEEAKKADEAKKKAEEAKKK--ADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKAdeLKKaE 1555
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  632 ILKRESKKTKLERLNSALSPKDCQDPAAVSAGSGSRPSSDVHAGLGElthGSVETQETQPKKAIPSKPQPKQLQLLEN-- 709
Cdd:PTZ00121  1556 ELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYE---EEKKMKAEEAKKAEEAKIKAEELKKAEEek 1632
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  710 ------QGPEKEEVRK-NYCRPREEPAEHRAGQEKPhggNAEEklgiDIDHTQSYRKQMEQSRRK----QRMEMEIAKAE 778
Cdd:PTZ00121  1633 kkveqlKKKEAEEKKKaEELKKAEEENKIKAAEEAK---KAEE----DKKKAEEAKKAEEDEKKAaealKKEAEEAKKAE 1705
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  779 KFgspKKDVDDYERRSlvHEVGKPPQDVTDDSPPSKKrrtdhvdfdictKRERNYRSSRQISEDSERTSCSPSVRHGSFH 858
Cdd:PTZ00121  1706 EL---KKKEAEEKKKA--EELKKAEEENKIKAEEAKK------------EAEEDKKKAEEAKKDEEEKKKIAHLKKEEEK 1768
                          650       660       670
                   ....*....|....*....|....*....|....
gi 1907156703  859 DDDDPRGSPRLVSVKGSPKGDEKGLPYPNAAVRD 892
Cdd:PTZ00121  1769 KAEEIRKEKEAVIEEELDEEDEKRRMEVDKKIKD 1802
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
121-183 1.95e-08

RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins; This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function.


Pssm-ID: 409682 [Multi-domain]  Cd Length: 91  Bit Score: 54.16  E-value: 1.95e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703  121 LSSNVSDQYLTRHFCRYGPV--VKVVFDRL----KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDF 183
Cdd:cd12236      9 LSYDTTESKLRREFEKYGPIkrVRLVRDKKtgksRGYAFIEFEHERDMKAAYKHADGKKIDGRRVLVDV 77
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
37-178 2.06e-08

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 59.82  E-value: 2.06e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLgfGKSMP-- 112
Cdd:TIGR01628   91 IFVKNLDKSVDNKALFDTFSKFGNILSCKVaTDENGKSRgYGFVHFEKEESAKAAIQKVNGMLLNDKEVYV--GRFIKkh 168
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  113 ----------TNcVWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRL-----KGMALVLYSEIEDAQAAVKETKGRKIGGN 177
Cdd:TIGR01628  169 ereaaplkkfTN-LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDgsgrsRGFAFVNFEKHEDAAKAVEEMNGKKIGLA 247

                   .
gi 1907156703  178 K 178
Cdd:TIGR01628  248 K 248
RRM3_Spen cd12310
RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily ...
116-185 2.06e-08

RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409750 [Multi-domain]  Cd Length: 72  Bit Score: 53.44  E-value: 2.06e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGN--KIKVDFAN 185
Cdd:cd12310      1 LWVGGLGPWTSLAELEREFDRFGAIRKIDYRKGDDYAYILYESLDAAQAAVRALRGFPLGGPdrRLRVDFAD 72
RRM_PPIL4 cd12235
RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and ...
36-110 2.52e-08

RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins; This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus.


Pssm-ID: 409681 [Multi-domain]  Cd Length: 83  Bit Score: 53.43  E-value: 2.52e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGKS 110
Cdd:cd12235      5 VLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVirdKKTGDSLQYAFIEFETKESCEEAYFKMDNVLIDDRRIHVDFSQS 82
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
120-184 3.12e-08

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 52.94  E-value: 3.12e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703  120 GLSSNVSDQYLTRHFCRYGPV--VKVVFDRL----KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd21608      6 NLSWDTTEDDLRDLFSEFGEVesAKVITDREtgrsRGFGFVTFSTAEAAEAAIDALNGKELDGRSIVVNEA 76
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
121-184 3.15e-08

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 52.94  E-value: 3.15e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703  121 LSSNVSDQYLTRHFCRYGPVVKVVF-----DRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12414      7 LPFKCTEDDLKKLFSKFGKVLEVTIpkkpdGKLRGFAFVQFTNVADAAKAIKGMNGKKIKGRPVAVDWA 75
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
34-110 9.53e-08

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 409670 [Multi-domain]  Cd Length: 84  Bit Score: 51.91  E-value: 9.53e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   34 TRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--------KKVNGVPqyAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 105
Cdd:cd12223      1 TTNLYVGNLPPSVTEEVLLREFGRFGPLASVKImwprteeeRRRNRNC--GFVAFMSRADAERAMRELNGKDVMGYELKL 78

                   ....*
gi 1907156703  106 GFGKS 110
Cdd:cd12223     79 GWGKA 83
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
116-186 1.04e-07

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 51.48  E-value: 1.04e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYGPVVKV-VFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANR 186
Cdd:cd12373      2 VYVGNLGPRVTKRELEDAFEKYGPLRNVwVARNPPGFAFVEFEDPRDAEDAVRALDGRRICGSRVRVELSRG 73
PHA03247 PHA03247
large tegument protein UL36; Provisional
2521-3046 1.14e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 58.41  E-value: 1.14e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2521 PANLGPTLTPHHPPALP------------SKLPAEVNHVPSGPSTPADRTIAHLATPKPDTHSPRPTGPT-------PGL 2581
Cdd:PHA03247  2512 PSRLAPAILPDEPVGEPvhprmltwirglEELASDDAGDPPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAvtsrarrPDA 2591
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2582 FPRPCHPSSTTSTALSTNATVMLAAGIPVPqfissiHPEQSVIMPPHSITQTVSLGHLSQGEVRMSTPTLPSITYSIRPE 2661
Cdd:PHA03247  2592 PPQSARPRAPVDDRGDPRGPAPPSPLPPDT------HAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPR 2665
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2662 TLHSPRAPLQPQQiEARAPQRVGTPqPATTGVPALATQHPPEEEVHyhlPVARAAAPVQSEVLVMQSEYRLHPYT----- 2736
Cdd:PHA03247  2666 RARRLGRAAQASS-PPQRPRRRAAR-PTVGSLTSLADPPPPPPTPE---PAPHALVSATPLPPGPAAARQASPALpaapa 2740
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2737 ---------VPRDVRIMVHPHVTAVSEQPRATEGVVKVPPANKAPQQLVKEAVKTSDAKAVPAPAPVPVPVPVPTPAPPP 2807
Cdd:PHA03247  2741 ppavpagpaTPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPP 2820
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2808 HGEARILTVTPSSQLQGLPLTPPVVVTHGVQIVHSSGELFQEYRYGDVRTyhAPAQQLTHTQFPVASSISLA-SRTKTSA 2886
Cdd:PHA03247  2821 AASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRS--PAAKPAAPARPPVRRLARPAvSRSTESF 2898
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2887 QVPPEGEPLQSTQSAQPAPSTQATqpiPPAPPCQPSQLSQPAQPPSGKIPQVSQEAKGTQTGGVEQTRLPAIPTNRPSEP 2966
Cdd:PHA03247  2899 ALPPDQPERPPQPQAPPPPQPQPQ---PPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVP 2975
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2967 HAQL--QRAPVETAQPAHPSPVSVSMkPDLPSPLSSQA----------APKQPLFVPANSGPSTPPGLALPHAE------ 3028
Cdd:PHA03247  2976 RFRVpqPAPSREAPASSTPPLTGHSL-SRVSSWASSLAlheetdpppvSLKQTLWPPDDTEDSDADSLFDSDSErsdlea 3054
                          570
                   ....*....|....*...
gi 1907156703 3029 VQPAPKQESSPHGTPQRP 3046
Cdd:PHA03247  3055 LDPLPPEPHDPFAHEPDP 3072
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
33-109 1.34e-07

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 51.24  E-value: 1.34e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703   33 ATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVpqyAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 109
Cdd:cd12262      2 ASRNVYVGNLDDSLTEEEIRGILEKYGEIESIKILKEKNC---AFVNYLNIANAIKAVQELPIKNPKFKKVRINYGK 75
RRM_SCAF4_SCAF8 cd12227
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), ...
33-105 1.58e-07

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs.


Pssm-ID: 409674 [Multi-domain]  Cd Length: 77  Bit Score: 50.90  E-value: 1.58e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907156703   33 ATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVpqyAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 105
Cdd:cd12227      1 CSTTLWVGHLSKKVTQEELKNLFEEYGEIQSIDMIPPRGC---AYVCMKTRQDAHRALQKLKNHKLRGKSIKI 70
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
120-186 1.77e-07

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 51.05  E-value: 1.77e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907156703  120 GLSSNVSDQYLTRHFCRYGPVvKVVF-------DRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANR 186
Cdd:cd12413      6 NLPYDTTDEQLEELFSDVGPV-KRCFvvkdkgkDKCRGFGYVTFALAEDAQRALEEVKGKKFGGRKIKVELAKK 78
RRM_RBM8 cd12324
RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; ...
116-184 2.36e-07

RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain).


Pssm-ID: 409762 [Multi-domain]  Cd Length: 88  Bit Score: 50.69  E-value: 2.36e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFDR----LKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12324      9 IFVTGVHEEAQEEDIHDKFAEFGEIknLHLNLDRrtgfVKGYALVEYETKKEAQAAIEGLNGKELLGQTISVDWA 83
RRM_G3BP cd12229
RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, ...
37-103 2.56e-07

RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins; This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif).


Pssm-ID: 409676 [Multi-domain]  Cd Length: 81  Bit Score: 50.49  E-value: 2.56e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGV---PQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 103
Cdd:cd12229      6 LFVGNLPHDITEDELKEFFSRFGNVLELRINSKGGGgrlPNFGFVVFDDPEAVQKILANKPIMFRGEHRL 75
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
35-104 3.43e-07

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 50.02  E-value: 3.43e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLK 104
Cdd:cd12392      3 NKLFVKGLPFSCTKEELEELFKQHGTVKDVRLvTYRNGKPKgLAYVEYENEADASQAVLKTDGTEIKDHTIS 74
RRM_TRA2A cd12642
RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and ...
112-184 3.47e-07

RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins; This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 410047 [Multi-domain]  Cd Length: 84  Bit Score: 50.37  E-value: 3.47e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703  112 PTNCVWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD----RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12642      3 PNTCLGVFGLSLYTTERDLREVFSRYGPLagVNVVYDqrtgRSRGFAFVYFERIDDSKEAMERANGMELDGRRIRVDYS 81
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
36-108 4.17e-07

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 49.59  E-value: 4.17e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFG 108
Cdd:cd12354      2 TVYVGNITKGLTEALLQQTFSPFGQILEVRVFPDKG---YAFIRFDSHEAATHAIVSVNGTIINGQAVKCSWG 71
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
116-180 4.28e-07

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 49.54  E-value: 4.28e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD---RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIK 180
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIksIRLVRDetgRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
130-184 7.56e-07

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 48.98  E-value: 7.56e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703  130 LTRHFCRYGPVVKVvfDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12233     17 IEKLFEPFGPLVRC--DIRKTFAFVEFEDSEDATKALEALHGSRIDGSVLTVEFV 69
RRM_RBM22 cd12224
RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This ...
35-109 7.58e-07

RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines.


Pssm-ID: 409671 [Multi-domain]  Cd Length: 74  Bit Score: 48.82  E-value: 7.58e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIkkvngVP--QYAFLQYCDIASVCKAIKKMDGE-YLGNNRLKLGFGK 109
Cdd:cd12224      2 TTLYVGGLGDKITEKDLRDHFYQFGEIRSITV-----VArqQCAFVQFTTRQAAERAAERTFNKlIIKGRRLKVKWGR 74
RRM2_RIM4_like cd12454
RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins; ...
34-80 8.89e-07

RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409888 [Multi-domain]  Cd Length: 80  Bit Score: 49.01  E-value: 8.89e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1907156703   34 TRTLFIGNLEKTTTYHDLRNIFQRFGEIVDID-IKKVNGVPQYAFLQY 80
Cdd:cd12454      3 KLSIFVGQLDPKTTDSELFRRFSKYGKIVDCKlIKRPEPVNAFAFLRF 50
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
37-104 1.24e-06

RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins; This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts.


Pssm-ID: 409797 [Multi-domain]  Cd Length: 73  Bit Score: 48.38  E-value: 1.24e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIV------DIDIKKVNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLK 104
Cdd:cd12362      1 LFVYHLPNEFTDQDLYQLFAPFGNVVsakvfvDKNTGRSKG---FGFVSYDNPLSAQAAIKAMNGFQVGGKRLK 71
RRM_RBMX_like cd12382
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y ...
116-184 1.49e-06

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins; This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G.


Pssm-ID: 409816 [Multi-domain]  Cd Length: 80  Bit Score: 48.17  E-value: 1.49e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVF------DRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12382      4 LFIGGLNTETNEKALEAVFGKYGRIVEVLLmkdretNKSRGFAFVTFESPADAKDAARDMNGKELDGKAIKVEQA 78
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
36-105 2.03e-06

RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409757 [Multi-domain]  Cd Length: 80  Bit Score: 47.99  E-value: 2.03e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVPQ----YAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 105
Cdd:cd12318      2 TLFVKNLNFKTTEEALKKHFEKCGPIRSVTIakKKDPKGPLlsmgYGFVEFKSPEAAQKALKQLQGTVLDGHALEL 77
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
37-103 2.17e-06

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 47.63  E-value: 2.17e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 103
Cdd:cd12417      2 LWISGLSDTTKAADLKKIFSKYGKVVSAKVvtsARTPGSRCYGYVTMASVEEADLCIKSLNKTELHGRVI 71
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
37-108 2.25e-06

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 47.62  E-value: 2.25e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK--VNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFG 108
Cdd:cd12284      1 LYVGSLHFNITEDMLRGIFEPFGKIEFVQLQKdpETGRSKgYGFIQFRDAEDAKKALEQLNGFELAGRPMKVGHV 75
RRM1_CoAA cd12608
RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator ...
37-103 2.42e-06

RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410020 [Multi-domain]  Cd Length: 69  Bit Score: 47.49  E-value: 2.42e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKvngvpQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 103
Cdd:cd12608      3 IFVGNVDEDTSQEELSALFEPYGAVLSCAVMK-----QFAFVHMRGEAAADRAIRELNGRELHGRAL 64
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
35-103 2.67e-06

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 47.64  E-value: 2.67e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---------KKVNGvpqYAFLQYCDIASVCKAIkKMDGEYLGNNRL 103
Cdd:cd12298      1 REIRVRNLDFELDEEALRGIFEKFGEIESINIpkkqknrkgRHNNG---FAFVTFEDADSAESAL-QLNGTLLDNRKI 74
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
134-181 2.78e-06

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.


Pssm-ID: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 47.28  E-value: 2.78e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1907156703  134 FCRYGPVVKV--VFDRL----KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 181
Cdd:cd12393     22 FSKYGKVVKVtiLKDKEtrksKGVAFVLFLDRESAHNAVRAMNNKELFGRTLKC 75
RRM_TRA2B cd12641
RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and ...
112-184 2.90e-06

RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins; This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes.


Pssm-ID: 410046 [Multi-domain]  Cd Length: 87  Bit Score: 47.69  E-value: 2.90e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703  112 PTNCVWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD----RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12641      6 PNCCLGVFGLSLYTTERDLREVFSKYGPIadVSIVYDqqsrRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 84
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
121-185 3.07e-06

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409884 [Multi-domain]  Cd Length: 78  Bit Score: 47.40  E-value: 3.07e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703  121 LSSNVSDQYLTRHFCRYGPVVKVVF------DRLKGMALVLYSEIEDAQAAVkETKGRKIGGNKIKVDFAN 185
Cdd:cd12450      7 LSWSATQDDLENFFSDCGEVVDVRIamdrddGRSKGFGHVEFASAESAQKAL-EKSGQDLGGREIRLDLAN 76
RRM_RNPS1 cd12365
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ...
37-98 3.18e-06

RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.


Pssm-ID: 409800 [Multi-domain]  Cd Length: 73  Bit Score: 47.16  E-value: 3.18e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDID--IKKVNGVP-QYAFLQYCDIASVCKAIKKMDGEYL 98
Cdd:cd12365      1 LHVGKLTRNVTKDHLKEIFSVYGTVKNVDlpIDREPNLPrGYAYVEFESPEDAEKAIKHMDGGQI 65
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
122-184 3.48e-06

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 47.27  E-value: 3.48e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703  122 SSNVSDQYLTRHFCRYGPVvKVVFDRLK--GMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12524     10 NSSVEDEELRALFEQFGEI-RTLYTACKhrGFIMVSYYDIRAAQSAKRALQGTELGGRKLDIHFS 73
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
121-184 3.57e-06

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 47.05  E-value: 3.57e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  121 LSSNVSDQYLTRHFCRYGPVVKV---VFD---RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12397      6 LSFETTEEDLRKHFAPAGKIRKVrmaTFEdsgKCKGFAFVDFKEIESATNAVKGPINHSLNGRDLRVEYG 75
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
34-112 4.11e-06

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 46.89  E-value: 4.11e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   34 TRTLFIGNLEKTTTYHDLRNIFQRFGEIVDI-DIKKVNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFgkSMP 112
Cdd:cd12524      1 SRTLFVRNINSSVEDEELRALFEQFGEIRTLyTACKHRG---FIMVSYYDIRAAQSAKRALQGTELGGRKLDIHF--SIP 75
RRM4_MRN1 cd12522
RNA recognition motif 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This ...
33-109 4.41e-06

RNA recognition motif 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409942 [Multi-domain]  Cd Length: 81  Bit Score: 47.14  E-value: 4.41e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   33 ATRTLFIGNLE--KTTTYHDLRNIFQRFGEivdidIKKVNGVPQY--AFLQYCDIASVCKAIKKMDGEYlGNNRLKLGFG 108
Cdd:cd12522      2 ASRNVYIGNIDdvRVLTEERLRHDFSQYGE-----IEQVNFLREKncAFVNFTNIANAIKAIDKIKSKP-YYKDLKINFG 75

                   .
gi 1907156703  109 K 109
Cdd:cd12522     76 K 76
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
37-104 5.04e-06

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.


Pssm-ID: 409751 [Multi-domain]  Cd Length: 73  Bit Score: 46.49  E-value: 5.04e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQ---YAFLQYCDIASVCKAIKKMDGEYLGNNRLK 104
Cdd:cd12311      1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTREsrgFAFVRFYDKRDAEDAIDAMDGAELDGRELR 71
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
37-104 6.30e-06

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.


Pssm-ID: 409779 [Multi-domain]  Cd Length: 66  Bit Score: 46.07  E-value: 6.30e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKvngvpQYAFLQYCDIASVCKAIKKMDGEYLGNNRLK 104
Cdd:cd12343      2 IFVGNLPDAATSEELRALFEKYGKVTECDIVK-----NYAFVHMEKEEDAEDAIKALNGYEFMGSRIN 64
RRM1_SRSF1 cd12597
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
37-107 6.39e-06

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 410010 [Multi-domain]  Cd Length: 79  Bit Score: 46.38  E-value: 6.39e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF 107
Cdd:cd12597      7 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF 77
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
34-189 7.13e-06

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 51.09  E-value: 7.13e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   34 TRTLFIGN-LEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVP-QYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 109
Cdd:TIGR01661    2 SKTNLIVNyLPQTMTQEEIRSLFTSIGEIESCKLvrDKVTGQSlGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  110 ----SMPTNCVWLDGLSSNVSDQYLTRHFCRYGPVVKV------VFDRLKGMALVLYSEIEDAQAAVKETKGRKIGG--N 177
Cdd:TIGR01661   82 pssdSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSrilsdnVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGctE 161
                          170
                   ....*....|..
gi 1907156703  178 KIKVDFANRESQ 189
Cdd:TIGR01661  162 PITVKFANNPSS 173
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
37-103 8.62e-06

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 46.14  E-value: 8.62e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQ------YAFLQYCDIASVCKAIKKMDGEYLGNNRL 103
Cdd:cd12355      2 LWIGNLDPRLTEYHLLKLLSKYGKIKKFDFLFHKTGPLkgqprgYCFVTFETKEEAEKAIECLNGKLALGKKL 74
sex-lethal TIGR01659
sex-lethal family splicing factor; This model describes the sex-lethal family of splicing ...
27-166 8.67e-06

sex-lethal family splicing factor; This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).


Pssm-ID: 273740 [Multi-domain]  Cd Length: 346  Bit Score: 50.79  E-value: 8.67e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   27 DEFHPKATRTLFIGN-LEKTTTYHDLRNIFQRFGEIVDIDIK---KVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNR 102
Cdd:TIGR01659   99 DDNDTNNSGTNLIVNyLPQDMTDRELYALFRTIGPINTCRIMrdyKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKR 178
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907156703  103 LKLGF----GKSMPTNCVWLDGLSSNVSDQYLTRHFCRYGPVVK--VVFDRL----KGMALVLYSEIEDAQAAV 166
Cdd:TIGR01659  179 LKVSYarpgGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQknILRDKLtgtpRGVAFVRFNKREEAQEAI 252
RRM_TUT1 cd12279
RNA recognition motif (RRM) found in speckle targeted PIP5K1A-regulated poly(A) polymerase ...
114-181 1.06e-05

RNA recognition motif (RRM) found in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins; This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS).


Pssm-ID: 409721 [Multi-domain]  Cd Length: 74  Bit Score: 45.87  E-value: 1.06e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703  114 NCVWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGM-ALVLYSEIEDAQAAVKETKgRKIGGNKIKV 181
Cdd:cd12279      3 RSVFVSGFKRGTSELELSDYFQAFGPVASVVMDKDKGVyAIVEMDSTETVEKVLSQPQ-HCLNGQRLRV 70
RRM2_PTBP1_hnRNPL_like cd12422
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
121-188 1.07e-05

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs.


Pssm-ID: 409856 [Multi-domain]  Cd Length: 85  Bit Score: 46.03  E-value: 1.07e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907156703  121 LSSNVSDQYLTRHFCRYGPVVK-VVFDRLKGM-ALVLYSEIEDAQAAVKETKGRKI--GGNKIKVDFANRES 188
Cdd:cd12422      9 LLYPVTVDVLHQVFSPYGAVEKiVIFEKGTGVqALVQFDSVESAEAAKKALNGRNIydGCCTLDIQFSRLKE 80
RRM4_I_PABPs cd12381
RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...
121-186 1.08e-05

RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409815 [Multi-domain]  Cd Length: 79  Bit Score: 45.72  E-value: 1.08e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703  121 LSSNVSDQYLTRHFCRYGPV--VKVVFD---RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANR 186
Cdd:cd12381      9 LDDTIDDEKLREEFSPFGTItsAKVMTDeggRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALAQR 79
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
34-104 1.09e-05

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 45.86  E-value: 1.09e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907156703   34 TRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIK--KVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLK 104
Cdd:COG0724      1 SMKIYVGNLPYSVTEEDLRELFSEYGEVTSVKLItdRETGRSRgFGFVEMPDDEEAQAAIEALNGAELMGRTLK 74
RRM_snRNP35 cd12237
RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein ...
36-112 1.50e-05

RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins; This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain.


Pssm-ID: 409683 [Multi-domain]  Cd Length: 94  Bit Score: 45.78  E-value: 1.50e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDI----DIkkVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF--G 108
Cdd:cd12237      6 TLFVGRLSLQTTEEKLKEVFSRYGDIRRLrlvrDI--VTGFSKrYAFIEYKEERDALHAYRDAKKLVIDQYEIFVDFecE 83

                   ....
gi 1907156703  109 KSMP 112
Cdd:cd12237     84 RTLP 87
RRM1_RIM4_like cd12453
RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; ...
112-186 1.51e-05

RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409887 [Multi-domain]  Cd Length: 86  Bit Score: 45.86  E-value: 1.51e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  112 PTNCVWLDGLSSNVSDQYL----TRHFCRYGPV--VKVVFDRL-KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12453      1 PSACLFVASLSSARSDEELcaavTNHFSKWGELlnVKVLKDWSnRPYAFVQYTNTEDAKNALVNGHNTLLDGRHLRVEKA 80

                   ....
gi 1907156703  185 --NR 186
Cdd:cd12453     81 kvNR 84
RRM3_RBM15B cd12558
RNA recognition motif 3 (RRM3) found in putative RNA-binding protein 15B (RBM15B) from ...
112-184 1.51e-05

RNA recognition motif 3 (RRM3) found in putative RNA-binding protein 15B (RBM15B) from vertebrate; This subgroup corresponds to the RRM3 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409974 [Multi-domain]  Cd Length: 76  Bit Score: 45.39  E-value: 1.51e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703  112 PTNCVWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGG--NKIKVDFA 184
Cdd:cd12558      1 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDYVKGDSFAYIQYESLDAAQAACAQMRGFPLGGpdRRLRVDFA 75
RRM2_SREK1 cd12260
RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 ...
35-104 1.59e-05

RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.


Pssm-ID: 409705 [Multi-domain]  Cd Length: 85  Bit Score: 45.76  E-value: 1.59e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVP-QYAFLQYCDIASVCKAIkKMDGEYLGNNRLK 104
Cdd:cd12260      5 RTVYVGNLDPSTTADQLLEFFSQAGEVKYVRMAGDETQPtRYAFVEFAEQTSVINAL-KLNGKMFGGRPLK 74
RRM_SRSF3 cd12645
RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 3 (SRSF3); ...
112-189 1.61e-05

RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 3 (SRSF3); This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 241089 [Multi-domain]  Cd Length: 81  Bit Score: 45.42  E-value: 1.61e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  112 PTNC-VWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDR-LKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANRESQ 189
Cdd:cd12645      2 PLDCkVYVGNLGNNGNKTELERAFGYYGPLRSVWVARnPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEKR 81
RRM3_Spen cd12310
RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily ...
37-109 1.92e-05

RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409750 [Multi-domain]  Cd Length: 72  Bit Score: 44.97  E-value: 1.92e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNgvpQYAFLQYCDIASVCKAIKKMDGEYLGNN--RLKLGFGK 109
Cdd:cd12310      1 LWVGGLGPWTSLAELEREFDRFGAIRKIDYRKGD---DYAYILYESLDAAQAAVRALRGFPLGGPdrRLRVDFAD 72
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
37-109 1.96e-05

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 45.13  E-value: 1.96e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDI------DIKKVNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 109
Cdd:cd12397      1 LFVGNLSFETTEEDLRKHFAPAGKIRKVrmatfeDSGKCKG---FAFVDFKEIESATNAVKGPINHSLNGRDLRVEYGE 76
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
113-181 2.14e-05

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409814 [Multi-domain]  Cd Length: 80  Bit Score: 44.86  E-value: 2.14e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907156703  113 TNcVWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD---RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 181
Cdd:cd12380      2 TN-VYVKNFGEDVDDDELKELFEKYGKItsAKVMKDdsgKSKGFGFVNFENHEAAQKAVEELNGKELNGKKLYV 74
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
37-95 2.33e-05

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 44.85  E-value: 2.33e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDG 95
Cdd:cd12414      2 LIVRNLPFKCTEDDLKKLFSKFGKVLEVTIpKKPDGKLRgFAFVQFTNVADAAKAIKGMNG 62
RRM1_HRB1_GBP2 cd21605
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, ...
36-96 2.39e-05

RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410184 [Multi-domain]  Cd Length: 77  Bit Score: 44.98  E-value: 2.39e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQ-YAFLQYCDIASVCKAIKKMDGE 96
Cdd:cd21605      3 SIFVGNLPFDCTWEDLKDHFSQVGEVIRADIVTSRGRHRgMGTVEFTNKEDVDRAISKFDHT 64
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
116-180 2.48e-05

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 44.62  E-value: 2.48e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIK 180
Cdd:cd12346      4 VFVGGLDPNVTEEDLRVLFGPFGEIVYVKIPPGKGCGFVQFVNRASAEAAIQKLQGTPIGGSRIR 68
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
36-109 2.73e-05

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 44.36  E-value: 2.73e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703   36 TLFIGNL-EKTTTYHDLRNIFQRFGEIVDIDIKKvngvpQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 109
Cdd:cd12233      1 TLFVVGFdPGTTREEDIEKLFEPFGPLVRCDIRK-----TFAFVEFEDSEDATKALEALHGSRIDGSVLTVEFVK 70
rne PRK10811
ribonuclease E; Reviewed
1192-1353 2.96e-05

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 50.04  E-value: 2.96e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1192 PKEAEKQEEPETHPKTPEPAAETKEPEPKAPVSAGLPAV-TVTVVTPEPASSAPEKAEEAAEAPSPAGEKPAepAPVSEE 1270
Cdd:PRK10811   850 PQDVQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVeAVAEVVEEPVVVAEPQPEEVVVVETTHPEVIA--APVTEQ 927
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1271 TKLVSEPASVPVEQPRQSDVPPGEDSRDSQDSAALAPSAPQ-----ESAATDAVPCVnAEPLTPGTTVSQVESSVDPKPS 1345
Cdd:PRK10811   928 PQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVvvaepEVVAQPAAPVV-AEVAAEVETVTAVEPEVAPAQV 1006

                   ....*...
gi 1907156703 1346 SPQPLSKL 1353
Cdd:PRK10811  1007 PEATVEHN 1014
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
121-181 3.33e-05

RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins; This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts.


Pssm-ID: 409797 [Multi-domain]  Cd Length: 73  Bit Score: 44.14  E-value: 3.33e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703  121 LSSNVSDQYLTRHFCRYGPVV--KVVFDRL----KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 181
Cdd:cd12362      6 LPNEFTDQDLYQLFAPFGNVVsaKVFVDKNtgrsKGFGFVSYDNPLSAQAAIKAMNGFQVGGKRLKV 72
RRM_U2AF35_like cd12287
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ...
118-185 3.71e-05

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35) and similar proteins; This subfamily corresponds to the RRM in U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) which has been implicated in the recruitment of U2 snRNP to pre-mRNAs. It is a highly conserved heterodimer composed of large and small subunits; this family includes the small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa subunit B (U2AF35B or C3H60). U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF (U2AF65 or U2AF2). Although the biological role of U2AF35B remains unclear, it shows high sequence homolgy to U2AF35, which contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR) -rich segment interrupted by glycines. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants.


Pssm-ID: 409729 [Multi-domain]  Cd Length: 101  Bit Score: 44.95  E-value: 3.71e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  118 LDGLSSNVSDQYLTRHF-----------CRYGPVVKVVF-----DRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 181
Cdd:cd12287     18 LDDGSLTLSEEEIQEHFdefyedvflelSRFGEIEDLVVcsnlnDHLLGNVYVKFESEEDAEAALQALNGRYYAGRPLYP 97

                   ....
gi 1907156703  182 DFAN 185
Cdd:cd12287     98 ELSP 101
RRM1_SF2_plant_like cd12599
RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar ...
36-105 3.99e-05

RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar proteins; This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2.


Pssm-ID: 410011 [Multi-domain]  Cd Length: 72  Bit Score: 43.97  E-value: 3.99e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 105
Cdd:cd12599      1 RVYVGNLPMDIREREVEDLFSKYGPVVSIDLKIPPRPPAYAFVEFEDARDAEDAIRGRDGYDFDGHRLRV 70
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
112-186 4.00e-05

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 44.14  E-value: 4.00e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  112 PTNCVWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFDRL---KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANR 186
Cdd:cd12412      1 IPNRIFVGGIDWDTTEEELREFFSKFGKVkdVKIIKDRAgvsKGYGFVTFETQEDAEKIQKWGANLVFKGKKLNVGPAIR 80
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
37-104 4.01e-05

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 44.16  E-value: 4.01e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKvnGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLK 104
Cdd:cd12373      2 VYVGNLGPRVTKRELEDAFEKYGPLRNVWVAR--NPPGFAFVEFEDPRDAEDAVRALDGRRICGSRVR 67
RRM_Aly_REF_like cd12418
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ...
116-181 4.13e-05

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.


Pssm-ID: 409852 [Multi-domain]  Cd Length: 75  Bit Score: 44.11  E-value: 4.13e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD---RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 181
Cdd:cd12418      3 VRVSNLHPDVTEEDLRELFGRVGPVksVKINYDrsgRSTGTAYVVFERPEDAEKAIKQFDGVLLDGQPMKV 73
PRK14949 PRK14949
DNA polymerase III subunits gamma and tau; Provisional
1191-1361 5.90e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237863 [Multi-domain]  Cd Length: 944  Bit Score: 48.95  E-value: 5.90e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1191 KPKE-AEKQEEPETHPKTPePAAETKEPEPKAPVSagLPAVTVTVVTPEPAssapekaeeaaeapspagEKPAEPAPVSE 1269
Cdd:PRK14949   630 SPKEgDGKKSSADRKPKTP-PSRAPPASLSKPASS--PDASQTSASFDLDP------------------DFELATHQSVP 688
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1270 ETKLVSEPASVPVEQPRQSDVPPGEDsrdsQDSAALAPSAPQESAATDAVPCVNAEPLTPGTTVSQV---ESSVDPKPSS 1346
Cdd:PRK14949   689 EAALASGSAPAPPPVPDPYDRPPWEE----APEVASANDGPNNAAEGNLSESVEDASNSELQAVEQQathQPQVQAEAQS 764
                          170
                   ....*....|....*
gi 1907156703 1347 PQPLSKLTQRSEEAE 1361
Cdd:PRK14949   765 PASTTALTQTSSEVQ 779
PHA03247 PHA03247
large tegument protein UL36; Provisional
1694-2214 5.91e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 49.17  E-value: 5.91e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1694 EAGPAAASPqeSESPQKGSGSSPQLANNPADPDREAEEESASASTAPPEGTQLARQIElEQAVQNIAKLPEPSAAAASKG 1773
Cdd:PHA03247  2486 ARFPFAAGA--APDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLTWIRGLE-ELASDDAGDPPPPLPPAAPPA 2562
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1774 TATATAASEEPAPEHGhKPAHQASETELAA----AIGSIISDASGEPENFSAPPSVPPGSQTHPREGMEPGLHEAESGIL 1849
Cdd:PHA03247  2563 APDRSVPPPRPAPRPS-EPAVTSRARRPDAppqsARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPH 2641
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1850 ETGTATESSAPQVSAL--------------DPPEGSADTKETR--------GNSGDSVQ-EAKGSKVEVTPPRKDKGRQK 1906
Cdd:PHA03247  2642 PPPTVPPPERPRDDPApgrvsrprrarrlgRAAQASSPPQRPRrraarptvGSLTSLADpPPPPPTPEPAPHALVSATPL 2721
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1907 TTRRRKRNANKKVVAITETRASEAEQTQSESPAAEEATAATPEAPQEEKQSEKPPSPPAECTFDPSKTPPAESLSQENSA 1986
Cdd:PHA03247  2722 PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSP 2801
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1987 AEKTPCKAPVL---PALPPLSQPALMDDGPQArfkvhsiieSDPVTPPSDSGIPPPTIPLVTiAKLPPPVIPGGVPHQSP 2063
Cdd:PHA03247  2802 WDPADPPAAVLapaAALPPAASPAGPLPPPTS---------AQPTAPPPPPGPPPPSLPLGG-SVAPGGDVRRRPPSRSP 2871
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2064 PPKVTEwitrQEEPRAQSTPSPALPPDTKAsdmdtssstlrkiLMDPKYVSATGVTSTSVTSAIAEPVSAPCLQEAPAPP 2143
Cdd:PHA03247  2872 AAKPAA----PARPPVRRLARPAVSRSTES-------------FALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPP 2934
                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703 2144 CDPKHPPlegvsaAAVPNADTQASEVPVAADKEKVAPVIAPkitsviSRMPVSIDLENSQKITLAKPAPQT 2214
Cdd:PHA03247  2935 PPPRPQP------PLAPTTDPAGAGEPSGAVPQPWLGALVP------GRVAVPRFRVPQPAPSREAPASST 2993
SPOC_FPA-like cd21546
SPOC (Spen paralog and ortholog C-terminal) domain found in Arabidopsis thaliana flowering ...
3060-3204 6.70e-05

SPOC (Spen paralog and ortholog C-terminal) domain found in Arabidopsis thaliana flowering time control protein FPA and similar proteins; FPA plays a role in the regulation of flowering time in the autonomous flowering pathway by decreasing FLOWERING LOCUS C mRNA levels. It is required for RNA-mediated chromatin silencing of a range of loci in the genome. FPA cotranscriptionally recognizes aberrant RNA and marks it for silencing. It controls alternative cleavage and polyadenylation on pre-mRNAs and antisense RNAs. FPA functions redundantly with FCA to prevent the expression of distally polyadenylated antisense RNAs at the FLC locus. FPA belongs to the Spen (split end) protein family, whose members contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439209  Cd Length: 125  Bit Score: 44.98  E-value: 6.70e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3060 VWQGLLAlKNDT--AAVQLHFVSGNNVLAHRSLPlseggPPLRIAQRMRLEASQLEGVARRMtvetdyCLLLALPCGRDQ 3137
Cdd:cd21546      1 KWSGTLA-KSGKprCNVVAHPVSGDVAREPVSLP-----EVLNVSHRTDLEEVAHKPVARAV------LVLLFAPENESD 68
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3138 EDVVSQteslkaaFITYLQAKQAAGIINVPnpgsnqPAYVLQIFPPCEFSESHLSRLAPD---LLASISN 3204
Cdd:cd21546     69 RGAFDE-------FIDYLSSKDRAGVVKLP------DNRTLYLVPPSEELFSQLLLNVIRqncLLGIVLP 125
RRM1_TIA1_like cd12352
RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and ...
121-184 6.85e-05

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409788 [Multi-domain]  Cd Length: 73  Bit Score: 43.55  E-value: 6.85e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907156703  121 LSSNVSDQYLTRHFCRYGPV--VKVVFDRLKG--MALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12352      6 LDRQVTEDLILQLFSQIGPCksCKMITEHGGNdpYCFVEFYEHNHAAAALQAMNGRKILGKEVKVNWA 73
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
35-95 7.03e-05

RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins; This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function.


Pssm-ID: 409682 [Multi-domain]  Cd Length: 91  Bit Score: 43.76  E-value: 7.03e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVPQ-YAFLQYCDIASVCKAIKKMDG 95
Cdd:cd12236      2 KTLFVARLSYDTTESKLRREFEKYGPIKRVRLvrDKKTGKSRgYAFIEFEHERDMKAAYKHADG 65
RRM2_Nop4p cd12675
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
128-184 7.08e-05

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410076 [Multi-domain]  Cd Length: 83  Bit Score: 43.62  E-value: 7.08e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907156703  128 QYLTRHFCRYGPVVKVVFDR-----LKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12675     16 VHLKKLFGRYGKVVEATIPRkkggkLSGFAFVTMKGRKNAEEALESVNGLEIDGRPVAVDWA 77
RRM_SNP1_like cd21615
RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ...
35-95 7.22e-05

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410194 [Multi-domain]  Cd Length: 118  Bit Score: 44.61  E-value: 7.22e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDG 95
Cdd:cd21615     19 KTLFVGRLDYSLTELELQKKFSKFGEIEKIRIvrdKETGKSRGYAFIVFKSESDAKNAFKEGNG 82
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
105-188 7.49e-05

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 45.41  E-value: 7.49e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  105 LGFGKSMPTNcVWLDGLSSNVSDQYLTRHFCRYGPVV--KVVFDR----LKGMALVLYSEIEDAQAAVKETKGRKIGGNK 178
Cdd:PLN03134    27 LGSLRLMSTK-LFIGGLSWGTDDASLRDAFAHFGDVVdaKVIVDRetgrSRGFGFVNFNDEGAATAAISEMDGKELNGRH 105
                           90
                   ....*....|
gi 1907156703  179 IKVDFANRES 188
Cdd:PLN03134   106 IRVNPANDRP 115
RRM3_RBM15 cd12557
RNA recognition motif 3 (RRM3) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
116-185 7.95e-05

RNA recognition motif 3 (RRM3) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM3 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contains three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralogue and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.


Pssm-ID: 409973 [Multi-domain]  Cd Length: 73  Bit Score: 43.39  E-value: 7.95e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGG--NKIKVDFAN 185
Cdd:cd12557      2 LWVGGLGPWVPLAALAREFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGpdRRLRVDFAD 73
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
35-105 8.27e-05

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409849 [Multi-domain]  Cd Length: 83  Bit Score: 43.36  E-value: 8.27e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEI--VDIDIKKVNGVPQ-YAFLQYCDIASVCKAIK------KMDGEYLGNNRLKL 105
Cdd:cd12415      1 KTVFIRNLSFDTTEEDLKEFFSKFGEVkyARIVLDKDTGHSKgTAFVQFKTKESADKCIEaandesEDGGLVLDGRKLIV 80
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
1153-1430 9.06e-05

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 48.63  E-value: 9.06e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1153 ASEGANSTSDSVQEPVVlfhsrfMELTRMQQKEKEKDQKPKEAEKQEEPETHPKTPEPAAETKEPEPKAPVSAGLPAVTV 1232
Cdd:PHA03307    57 AGAAACDRFEPPTGPPP------GPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPASPPPSP 130
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1233 TVVTPEPASSAPEKAEEAAEAPSPAGEKPAEPAPVSEETKLVSEPASVPvEQPRQSDVPPGEDSRDSQDSAALAPSAPQE 1312
Cdd:PHA03307   131 APDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAALPLSSP-EETARAPSSPPAEPPPSTPPAAASPRPPRR 209
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1313 SaATDAVPCVNAEPLTPGTTVSQVESSVDPKPSSPQPLSKLTQRSE----------------EAEEGKVEKPDTTPSTEP 1376
Cdd:PHA03307   210 S-SPISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENEcplprpapitlptriwEASGWNGPSSRPGPASSS 288
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1907156703 1377 DATqnagvaSEAQPPASEDVEANPPVAAKDRKTNKSKRSKTSVQAAAASVVEKP 1430
Cdd:PHA03307   289 SSP------RERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESS 336
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
37-105 9.65e-05

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 43.17  E-value: 9.65e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 105
Cdd:cd12448      1 LFVGNLPFSATQDALYEAFSQHGSIVSVRLptdRETGQPKGFGYVDFSTIDSAEAAIDALGGEYIDGRPIRL 72
RRM2_MEI2_like cd12529
RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to ...
36-105 9.99e-05

RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409948 [Multi-domain]  Cd Length: 71  Bit Score: 42.88  E-value: 9.99e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVdiDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 105
Cdd:cd12529      3 TLVVFNLDPSISNDDLHQIFGAYGEIK--EIRETPNKRHHKFIEFYDVRSAEAALKALNKSEIAGKRIKL 70
RRM1_2_CID8_like cd12225
RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting ...
35-110 1.02e-04

RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.


Pssm-ID: 409672 [Multi-domain]  Cd Length: 76  Bit Score: 43.22  E-value: 1.02e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKmDGEYLGNNRLKLGFGKS 110
Cdd:cd12225      1 RTIHVGGIDGSLSEDELADYFSNCGEVTQVRLCGDRVHTRFAWVEFATDASALSALNL-DGTTLGGHPLRVSPSKT 75
RRM2_MEI2_EAR1_like cd12276
RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; ...
36-105 1.05e-04

RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 409718 [Multi-domain]  Cd Length: 71  Bit Score: 42.63  E-value: 1.05e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDI--DIKKVNgvpQYaFLQYCDIASVCKAIKKMDGEYLGNNRLKL 105
Cdd:cd12276      3 TLLVFNLDAPVSNDELKSLFSKFGEIKEIrpTPDKPS---QK-FVEFYDVRDAEAALDGLNGRELLGGKLKV 70
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
116-182 1.15e-04

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 42.78  E-value: 1.15e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVF------DRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVD 182
Cdd:cd12448      1 LFVGNLPFSATQDALYEAFSQHGSIVSVRLptdretGQPKGFGYVDFSTIDSAEAAIDALGGEYIDGRPIRLD 73
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
34-103 1.16e-04

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 42.90  E-value: 1.16e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907156703   34 TRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKV------NGVpQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 103
Cdd:cd21619      1 SNTIYVGNIDMTINEDALEKIFSRYGQVESVRRPPIhtdkadRTT-GFGFIKYTDAESAERAMQQADGILLGRRRL 75
RRM1_hnRNPA_hnRNPD_like cd12325
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and ...
37-95 1.18e-04

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins; This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs.


Pssm-ID: 409763 [Multi-domain]  Cd Length: 72  Bit Score: 42.51  E-value: 1.18e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK--VNGVPQ-YAFLQYCDIASVCKAIK----KMDG 95
Cdd:cd12325      1 LFVGGLSWETTEESLREYFSKYGEVVDCVVMKdpATGRSRgFGFVTFKDPSSVDAVLAarphTLDG 66
RRM2_CoAA cd12609
RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator ...
37-103 1.25e-04

RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410021 [Multi-domain]  Cd Length: 68  Bit Score: 42.53  E-value: 1.25e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIkkvngVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 103
Cdd:cd12609      3 IFVGNVSATCTSDELRGLFEEFGRVVECDK-----VKDYAFVHMEREEEALAAIEALNGKEVKGRRI 64
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
1208-1434 1.38e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 47.92  E-value: 1.38e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1208 PEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAGEKPAEPAPVS---EETKLVSEPASVPVEQ 1284
Cdd:PRK07003   374 ARVAGAVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPAtadRGDDAADGDAPVPAKA 453
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1285 PRQSDVPPGEDSRDSQDSAALAPSApqeSAATDAVPCVNAEPLTPGTTVSQVESSVDPKPSSPqplsKLTQRSEEAEEGK 1364
Cdd:PRK07003   454 NARASADSRCDERDAQPPADSGSAS---APASDAPPDAAFEPAPRAAAPSAATPAAVPDARAP----AAASREDAPAAAA 526
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703 1365 VEKPDTTPStEPDATQNAGVASEAQppASEDVEANPPV-AAKDRKTNKSKRSKtsvQAAAASVVEKPVTRK 1434
Cdd:PRK07003   527 PPAPEARPP-TPAAAAPAARAGGAA--AALDVLRNAGMrVSSDRGARAAAAAK---PAAAPAAAPKPAAPR 591
RRM1_hnRNPD_like cd12575
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, ...
37-96 1.41e-04

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins; This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 409989 [Multi-domain]  Cd Length: 72  Bit Score: 42.55  E-value: 1.41e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIK--KVNGVPQ-YAFLQYCDIASVCKAIK----KMDGE 96
Cdd:cd12575      1 MFIGGLSWDTSKKDLKDYFSKFGEVVDCTIKldPVTGRSRgFGFVLFKDAESVDKVLDqkehKLDGK 67
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
37-80 1.62e-04

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.


Pssm-ID: 409673 [Multi-domain]  Cd Length: 77  Bit Score: 42.56  E-value: 1.62e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQ--YAFLQY 80
Cdd:cd12226      2 LFVGGLSPSITEDDLERRFSRFGTVSDVEIIRKKDAPDrgFAYIDL 47
PTZ00121 PTZ00121
MAEBL; Provisional
1259-1764 1.62e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 47.83  E-value: 1.62e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1259 EKPAEPAPVSEETKLVSEPASVPVEQPRQSDVPPGEDSRDSQDSAALAPSAPQESAATDAVPcvNAEPLTPGTTVSQVES 1338
Cdd:PTZ00121  1223 AKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELK--KAEEKKKADEAKKAEE 1300
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1339 --SVDPKPSSPQPLSKLTQRSEEAEEGKvEKPDTTPSTEPDATQNAGVASEAQPPASEDVEANPPVA-AKDRKTNKSKRS 1415
Cdd:PTZ00121  1301 kkKADEAKKKAEEAKKADEAKKKAEEAK-KKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAeAAEKKKEEAKKK 1379
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1416 KTSVQAAAASVVEKPVTRKSERIDREKLKRSSSPRGEAQKLLELKMEAEKITRTASKSSGGDTEHPEPSLPLSRSRRRNV 1495
Cdd:PTZ00121  1380 ADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKA 1459
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1496 RSVYATMTDHESRSPAKEPVEQPRvTRKRLERELQEAvvppttprRGRPPKTRRRAEEDGEHERKEPAETPRPAEGWRSP 1575
Cdd:PTZ00121  1460 EEAKKKAEEAKKADEAKKKAEEAK-KADEAKKKAEEA--------KKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKA 1530
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1576 RSQKSAAAAgpqgkrgRNEQKVEAAAEAGAQASTREGNPKSRGEREAASEPKRDR--RDPSTDKNGPDTFPVEVLERKPP 1653
Cdd:PTZ00121  1531 EEAKKADEA-------KKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMalRKAEEAKKAEEARIEEVMKLYEE 1603
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1654 EKTYKSKrgRARSTRSAMDRAAHQRSLEMAARAAGQAADKEAGPAAASPQESESPQKGSGSSPQLANNPADPDREAEEES 1733
Cdd:PTZ00121  1604 EKKMKAE--EAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAK 1681
                          490       500       510
                   ....*....|....*....|....*....|.
gi 1907156703 1734 ASASTAPPEGTQLARQIELEQAVQNIAKLPE 1764
Cdd:PTZ00121  1682 KAEEDEKKAAEALKKEAEEAKKAEELKKKEA 1712
RRM1_PSRP2_like cd21609
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
121-184 1.80e-04

RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410188 [Multi-domain]  Cd Length: 80  Bit Score: 42.41  E-value: 1.80e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  121 LSSNVSDQYLTRHFCRYGPV--VKVVFDRL----KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd21609      7 IPRNVTSEELAKIFEEAGTVeiAEVMYDRYtgrsRGFGFVTMGSVEDAKAAIEKLNGTEVGGREIKVNIT 76
RRM_RBM42 cd12383
RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This ...
37-105 1.87e-04

RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409817 [Multi-domain]  Cd Length: 83  Bit Score: 42.65  E-value: 1.87e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 105
Cdd:cd12383      9 IFCGDLGNEVTDEVLARAFSKYPSFQKAKVirdKRTGKSKGYGFVSFKDPNDYLKALREMNGKYVGNRPIKL 80
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
37-95 1.90e-04

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 42.33  E-value: 1.90e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI------KKVNGVpqyAFLQYCDIASVCKAIKKMDG 95
Cdd:cd12316      2 LFVRNLPFTATEDELRELFEAFGKISEVHIpldkqtKRSKGF---AFVLFVIPEDAVKAYQELDG 63
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
37-97 2.03e-04

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.


Pssm-ID: 409796 [Multi-domain]  Cd Length: 77  Bit Score: 42.22  E-value: 2.03e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEY 97
Cdd:cd12361      2 LFVGMIPKTASEEDVRPLFEQFGNIEEVQIlrDKQTGQSKgCAFVTFSTREEALRAIEALHNKK 65
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
36-111 2.11e-04

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 42.14  E-value: 2.11e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   36 TLFIGNLEKTTTYHDLRN----IFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLgnnrlklgFGKSM 111
Cdd:cd12246      1 TLYINNLNEKIKKDELKRslyaLFSQFGPVLDIVASKSLKMRGQAFVVFKDVESATNALRALQGFPF--------YGKPM 72
RRM1_SRSF9 cd12598
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 9 ...
37-107 2.17e-04

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 9 (SRSF9); This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 241042 [Multi-domain]  Cd Length: 72  Bit Score: 42.09  E-value: 2.17e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF 107
Cdd:cd12598      2 IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGRNGYDFGQCRLRVEF 72
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
121-186 3.11e-04

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410075 [Multi-domain]  Cd Length: 80  Bit Score: 41.68  E-value: 3.11e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907156703  121 LSSNVSDQYLTRHFCRYGPV--VKVVFD----RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANR 186
Cdd:cd12674      8 LPFDVTLESLTDFFSDIGPVkhAVVVTDpetkKSRGYGFVSFSTHDDAEEALAKLKNRKLSGHILKLDFAKP 79
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
35-107 3.23e-04

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 41.73  E-value: 3.23e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIK--KVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF 107
Cdd:cd12398      1 RSVFVGNIPYDATEEQLKEIFSEVGPVVSFRLVtdRETGKPKgYGFCEFRDAETALSAVRNLNGYELNGRPLRVDF 76
RRM3_PES4_MIP6 cd21603
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ...
36-106 4.03e-04

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.


Pssm-ID: 410182 [Multi-domain]  Cd Length: 73  Bit Score: 41.12  E-value: 4.03e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGV-PQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLG 106
Cdd:cd21603      2 AIFVKNLPLDTNNDEILDFFSKVGPIKSVFTSPKYKYnSLWAFVTYKKGSDTEKAIKLLNGTLFKGRTIEVT 73
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
36-95 4.24e-04

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 41.39  E-value: 4.24e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIK--KVNGVPQ-YAFLQYCDIASVCKAIKKMDG 95
Cdd:cd21608      1 KLYVGNLSWDTTEDDLRDLFSEFGEVESAKVItdRETGRSRgFGFVTFSTAEAAEAAIDALNG 63
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
1121-1535 4.48e-04

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 46.22  E-value: 4.48e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1121 SSIFEQDSKRLQHLERKSEEPDLPPGGLYGRQASEGA---NSTSDSVQEPVVLFHSRFMELTR--------------MQQ 1183
Cdd:PTZ00449   497 APIEEEDSDKHDEPPEGPEASGLPPKAPGDKEGEEGEhedSKESDEPKEGGKPGETKEGEVGKkpgpakehkpskipTLS 576
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1184 KEKEKDQKPKEAEKQEEPEThPKTP-EPAAETKEPEPKAPVSAGLPAvtvtvvTPEPASSAPEKAEEAAEAPSPAGEKPA 1262
Cdd:PTZ00449   577 KKPEFPKDPKHPKDPEEPKK-PKRPrSAQRPTRPKSPKLPELLDIPK------SPKRPESPKSPKRPPPPQRPSSPERPE 649
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1263 EP-APVSEETKLVSEPASVPVEQPRQSDVPPGEDSRDSQDSAALAPSAPQESAATDAVPCVNAEPLT---------PGTT 1332
Cdd:PTZ00449   650 GPkIIKSPKPPKSPKPPFDPKFKEKFYDDYLDAAAKSKETKTTVVLDESFESILKETLPETPGTPFTtprplppklPRDE 729
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1333 VSQVESSVDPKPSSPQPLSKLTQRSEEAEEGKvEKPDTTPST--------EPDATQNAGVASEA--QPPASEDVEANPP- 1401
Cdd:PTZ00449   730 EFPFEPIGDPDAEQPDDIEFFTPPEEERTFFH-ETPADTPLPdilaeefkEEDIHAETGEPDEAmkRPDSPSEHEDKPPg 808
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1402 ----VAAKDRKTNKSKRSKTSVQAAAASVVEKPVTRKSeridreKLKRSSSPRGEAQKLLELKMEAEkITRTASKSSG-- 1475
Cdd:PTZ00449   809 dhpsLPKKRHRLDGLALSTTDLESDAGRIAKDASGKIV------KLKRSKSFDDLTTVEEAEEMGAE-ARKIVVDDDGte 881
                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1476 GDTEHPEPSlplsrsrrrnvrsVYATMTDHESRSPAKEPVEQPRVTRKRLERELQEAVVP 1535
Cdd:PTZ00449   882 ADDEDTHPP-------------EEKHKSEVRRRRPPKKPSKPKKPSKPKKPKKPDSAFIP 928
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
35-128 5.49e-04

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 45.68  E-value: 5.49e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQ---YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFG-KS 110
Cdd:TIGR01622  215 HRLYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKDPETGRskgYGFIQFRDAEQAKEALEKMNGFELAGRPIKVGLGnDF 294
                           90
                   ....*....|....*...
gi 1907156703  111 MPTNCVWLDGLSSNVSDQ 128
Cdd:TIGR01622  295 TPESDANLAQRFQDQDGS 312
Collagen_mid pfam15984
Bacterial collagen, middle region; Collagen_mid is the conserved central region of bacterial ...
2213-2291 5.71e-04

Bacterial collagen, middle region; Collagen_mid is the conserved central region of bacterial collagen triple helix repeat proteins.


Pssm-ID: 435053 [Multi-domain]  Cd Length: 198  Bit Score: 43.86  E-value: 5.71e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2213 QTLTGLVSALTGLVNVSLVPVNALKGPVKGSVATLKGLVSTPAGPVN--LLKGPVNVLTGPVNVLTTPVSATVG----TV 2286
Cdd:pfam15984   60 NAVTSAGQLVSGLGTGPLAPLAPVTTPLGGTVSTLGGAVTGGGTTLGtaLSTGPVQQLTQQVSSAITPITSTVTgttqTV 139

                   ....*
gi 1907156703 2287 NAAPG 2291
Cdd:pfam15984  140 GAATG 144
RRM2_MRN1 cd12523
RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This ...
33-93 5.82e-04

RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409943 [Multi-domain]  Cd Length: 78  Bit Score: 40.88  E-value: 5.82e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703   33 ATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVpqyAFLQYCDIASVCKAIKKM 93
Cdd:cd12523      2 ASRNVYLGNLPESITEEELREDLEKFGPIDQIKIVKEKNI---AFVHFLSIANAIKVVTTL 59
RRM1_hnRPDL cd12758
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP ...
37-104 5.84e-04

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 410152 [Multi-domain]  Cd Length: 76  Bit Score: 41.12  E-value: 5.84e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK--VNGVPQ-YAFLQYCDIASVCKAIK----KMDGEYLGNNRLK 104
Cdd:cd12758      2 MFIGGLSWDTSKKDLTEYLSRFGEVVDCTIKTdpVTGRSRgFGFVLFKDAASVDKVLElkehKLDGKLIDPKRAK 76
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
1378-1787 5.86e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 45.93  E-value: 5.86e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1378 ATQNAGVASEAQPPASEDVEANPPVAAKDRKTNKSKRSKTSV----QAAAASVVEKPVTRKSERIDREKLKRSSSPRGEA 1453
Cdd:PHA03307    12 EAAAEGGEFFPRPPATPGDAADDLLSGSQGQLVSDSAELAAVtvvaGAAACDRFEPPTGPPPGPGTEAPANESRSTPTWS 91
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1454 QKLLELKMEAEKITRTASKSSGGDTEH-------PEPSLPLSRSRRRNVRSVYATMTDHESRSPAKEPVEQPRVTRKRLE 1526
Cdd:PHA03307    92 LSTLAPASPAREGSPTPPGPSSPDPPPptpppasPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQ 171
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1527 REL-----QEAVVPPTTPRRGRPPKTRRRAEEDGEHERKEPAE------TPRPAEGWRSPRSQKSAAAAGPQGKR----G 1591
Cdd:PHA03307   172 AALplsspEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISasasspAPAPGRSAADDAGASSSDSSSSESSGcgwgP 251
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1592 RNEQKVEAAAEAGAQASTREGNPKSRGEREAASEPKRD---RRDPSTDKNGPDTFPvevlerKPPEKTYKSKRGRARSTR 1668
Cdd:PHA03307   252 ENECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSsprERSPSPSPSSPGSGP------APSSPRASSSSSSSRESS 325
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1669 SAMDRAAHQRSlemaaraagqaaDKEAGPAAASPQESESPQKGSGSSPqlannPADPDREAEEESASASTAPPEGTQL-- 1746
Cdd:PHA03307   326 SSSTSSSSESS------------RGAAVSPGPSPSRSPSPSRPPPPAD-----PSSPRKRPRPSRAPSSPAASAGRPTrr 388
                          410       420       430       440
                   ....*....|....*....|....*....|....*....|..
gi 1907156703 1747 -ARQIELEQAVQNIAKLPEPSAAAASKGTATATAASEEPAPE 1787
Cdd:PHA03307   389 rARAAVAGRARRRDATGRFPAGRPRPSPLDAGAASGAFYARY 430
RRM_hnRNPC_like cd12341
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C) ...
124-181 6.22e-04

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins; This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes.


Pssm-ID: 409778 [Multi-domain]  Cd Length: 68  Bit Score: 40.69  E-value: 6.22e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907156703  124 NVSDQYLTRHFCRYGPVVKVVFdrLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 181
Cdd:cd12341     12 QMTKEDLEEIFSKYGKILGISL--HKGYGFVQFDNEEDARAAVAGENGRTIKGQRLDI 67
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
2860-3052 6.48e-04

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 45.41  E-value: 6.48e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2860 APAQQLTHTQFPVASSISLASRTKTSAQvppEGEPLQSTQSAQPAPSTQATQPIPPAPPCQPSQLSQPAQPPSGKIPQVS 2939
Cdd:pfam09770  170 AAAPAPAPQPAAQPASLPAPSRKMMSLE---EVEAAMRAQAKKPAQQPAPAPAQPPAAPPAQQAQQQQQFPPQIQQQQQP 246
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2940 QEAKGtqtggveqtrlPAIPTNRPSEPHAQLQRAPVETAQPAHPSPVSVSmKPDLPSPLSSQAAPKQPL-----FVPANS 3014
Cdd:pfam09770  247 QQQPQ-----------QPQQHPGQGHPVTILQRPQSPQPDPAQPSIQPQA-QQFHQQPPPVPVQPTQILqnpnrLSAARV 314
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 1907156703 3015 GPSTPPGLALPHAEVQPAPKQESSPHGTPQ---RPVDMVQL 3052
Cdd:pfam09770  315 GYPQNPQPGVQPAPAHQAHRQQGSFGRQAPiitHPQQLAQL 355
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
134-184 6.50e-04

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 40.60  E-value: 6.50e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1907156703  134 FCRYGPVVKVVF---DRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12246     24 FSQFGPVLDIVAsksLKMRGQAFVVFKDVESATNALRALQGFPFYGKPMRIQYA 77
RRM_FET cd12280
RNA recognition motif (RRM) found in the FET family of RNA-binding proteins; This subfamily ...
116-183 6.62e-04

RNA recognition motif (RRM) found in the FET family of RNA-binding proteins; This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15.


Pssm-ID: 409722 [Multi-domain]  Cd Length: 82  Bit Score: 40.86  E-value: 6.62e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYG----------PVVKVVFDR----LKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 181
Cdd:cd12280      1 IFVSGLPPDVTIDELADLFGQIGiikrykdtwpPKIKIYTDKetgkPKGEATLTYEDPSAAKAAIEWFNGKEFRGNKIKV 80

                   ..
gi 1907156703  182 DF 183
Cdd:cd12280     81 SL 82
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
1190-1388 6.89e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 45.36  E-value: 6.89e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1190 QKPKEAEKQEEPETHPKTPEPAAETKEPEPKAPvsAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAGEKPAEPAPVSE 1269
Cdd:PRK07764   604 ASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAP--AEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAP 681
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1270 ETKLVS--------EPASVPVEQPRQSDVPPGEDSRDSQDSAALAPSAPQESAATDAVPcVNAEPLTPGTTVSQVESSVD 1341
Cdd:PRK07764   682 PPAPAPaapaapagAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVP-LPPEPDDPPDPAGAPAQPPP 760
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 1907156703 1342 PKPSSPQPLSKLTQRSEEAEEGKVEKPDTTPSTEPDATQNAGVASEA 1388
Cdd:PRK07764   761 PPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDDEDRRDAEEVAME 807
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
34-95 7.29e-04

RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409982 [Multi-domain]  Cd Length: 79  Bit Score: 40.86  E-value: 7.29e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703   34 TRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDG 95
Cdd:cd12566      2 TGRLFLRNLPYSTKEDDLQKLFSKFGEVSEVHVpidKKTKKSKGFAYVLFLDPEDAVQAYNELDG 66
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
1218-1407 7.30e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 45.23  E-value: 7.30e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1218 EPkAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAGEKPAEPAPVSEETKLVSEPASVPVEQPRQSDVPPGEdSR 1297
Cdd:PRK07003   359 EP-AVTGGGAPGGGVPARVAGAVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPA-TA 436
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1298 DSQDSAALAPSAPQESAATDAVPCVNAEPLTPgTTVSQVESSVDPKPSSPQPLSKltqrseEAEEGKVEKPDTTPSTEPD 1377
Cdd:PRK07003   437 DRGDDAADGDAPVPAKANARASADSRCDERDA-QPPADSGSASAPASDAPPDAAF------EPAPRAAAPSAATPAAVPD 509
                          170       180       190
                   ....*....|....*....|....*....|..
gi 1907156703 1378 ATQNAGVASE--AQPPASEDVEANPPVAAKDR 1407
Cdd:PRK07003   510 ARAPAAASREdaPAAAAPPAPEARPPTPAAAA 541
RRM1_SRSF5 cd12595
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 ...
37-105 7.95e-04

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 (SRSF5); This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain.


Pssm-ID: 410008 [Multi-domain]  Cd Length: 70  Bit Score: 40.31  E-value: 7.95e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKkvNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 105
Cdd:cd12595      2 VFIGRLNPAAREKDVERFFKGYGRIRDIDLK--RG---FGFVEFEDPRDADDAVYELDGKELCNERVTI 65
RRM_SCAF4_SCAF8 cd12227
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), ...
116-184 8.91e-04

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs.


Pssm-ID: 409674 [Multi-domain]  Cd Length: 77  Bit Score: 40.50  E-value: 8.91e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12227      5 LWVGHLSKKVTQEELKNLFEEYGEIQSIDMIPPRGCAYVCMKTRQDAHRALQKLKNHKLRGKSIKIAWA 73
RRM3_RBM39_like cd12285
RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
136-183 8.91e-04

RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs.


Pssm-ID: 409727 [Multi-domain]  Cd Length: 85  Bit Score: 40.61  E-value: 8.91e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1907156703  136 RYGPVVKVVFDRL--KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDF 183
Cdd:cd12285     34 KYGPVLHIYVDKNspQGNVYVKFKTIEAAQKCVQAMNGRWFDGRQITAAY 83
PTZ00121 PTZ00121
MAEBL; Provisional
1174-1695 8.99e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 45.13  E-value: 8.99e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1174 RFMELTRMQQKEKEKDQKPKEAEKQEEpetHPKTPEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEA 1253
Cdd:PTZ00121  1207 KAEEERKAEEARKAEDAKKAEAVKKAE---EAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADEL 1283
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1254 PSPAGEKPAEPAPVSEETKLVSEpASVPVEQPRQSDvPPGEDSRDSQDSAALAPSAPQESAATDAVPCVNAEpltpgTTV 1333
Cdd:PTZ00121  1284 KKAEEKKKADEAKKAEEKKKADE-AKKKAEEAKKAD-EAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAE-----AAA 1356
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1334 SQVESSVDPKPSSPQPLSKLTQRSEEAEEgKVEKPDTTPSTEPDATQNAGVASEAQPPASEDVEANppvAAKDRKTNKSK 1413
Cdd:PTZ00121  1357 DEAEAAEEKAEAAEKKKEEAKKKADAAKK-KAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKAD---EAKKKAEEKKK 1432
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1414 RSKTSVQAAAASVVEKPVTRKSERIDREKLKRSSSprgEAQKLLELKMEAEKiTRTASKSSGGDTEHPEPSLPLSRSRRR 1493
Cdd:PTZ00121  1433 ADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAE---EAKKADEAKKKAEE-AKKADEAKKKAEEAKKKADEAKKAAEA 1508
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1494 NVRSVYATMTDHesrspAKEPVEQPRVTRKRLERELQEAvvppttpRRGRPPKTRRRAEEDGEHERKEPAETPRPAEGWR 1573
Cdd:PTZ00121  1509 KKKADEAKKAEE-----AKKADEAKKAEEAKKADEAKKA-------EEKKKADELKKAEELKKAEEKKKAEEAKKAEEDK 1576
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1574 SPRSQKSAAAAGPQGKRGRNEQKVEAAAEAGAQASTR-EGNPKSRGEREAASEPKRDRRDPSTDKNGPDTFPVEVLeRKP 1652
Cdd:PTZ00121  1577 NMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKkAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEEL-KKA 1655
                          490       500       510       520
                   ....*....|....*....|....*....|....*....|...
gi 1907156703 1653 PEKTYKSKRGRARSTRSAMDRAAHQRSLEMAARAAGQAADKEA 1695
Cdd:PTZ00121  1656 EEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEA 1698
RRM_SRSF10 cd12559
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and ...
112-184 9.03e-04

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins; This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 409975 [Multi-domain]  Cd Length: 95  Bit Score: 40.81  E-value: 9.03e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703  112 PTNCVWLDGLSSNVSDQYLTRHFCRYGPVVKVVFD------RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12559      4 PNTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPldfytrRPRGFAYVQFEDVRDAEDALHNLDRKWICGRQIEIQFA 82
RRM_RBM7_like cd12336
RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This ...
35-105 1.01e-03

RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 409773 [Multi-domain]  Cd Length: 75  Bit Score: 39.98  E-value: 1.01e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK-VNGVP-QYAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 105
Cdd:cd12336      2 RTLFVGNLDPRVTEEILYELFLQAGPLEGVKIPKdPNGKPkNFAFVTFKHEVSVPYAIQLLNGIRLFGREIRI 74
RRM3_Crp79_Mug28 cd21622
RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, ...
37-110 1.02e-03

RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the three RRM motif.


Pssm-ID: 410201 [Multi-domain]  Cd Length: 92  Bit Score: 40.81  E-value: 1.02e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703   37 LFIGNLEKTTTYH--DLRNIFQRFGEIVDIDIKKVN--GVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGKS 110
Cdd:cd21622      6 LFVKNLDDTVITNkeDLEQLFSPFGQIVSSYLATYPgtGISKgFGFVAFSKPEDAAKAKETLNGVMVGRKRIFVSYAER 84
RRM1_CELF3_4_5_6 cd12632
RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
37-89 1.26e-03

RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.


Pssm-ID: 410041 [Multi-domain]  Cd Length: 87  Bit Score: 40.48  E-value: 1.26e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQY---AFLQYCDIASVCKA 89
Cdd:cd12632      8 LFIGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHkgcAFLTYCARESALKA 63
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
2925-3088 1.27e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 44.59  E-value: 1.27e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2925 SQPAQPPSGKIPQVSQEAKGTQTGGVEQTRLPAIPTNRPSEPHAQLQRAPVETAQPAHPSPVSVSMKPDLPSPLSSQAAP 3004
Cdd:PRK07764   394 PAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAA 473
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 3005 KQPLFVPANSGPSTPPGLALPHAEVQPAPKQESSPHGTPQR--PvDMVQLLKQKYPIVWQGLLA----LKNDTAAVQLHF 3078
Cdd:PRK07764   474 PEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDAATLRErwP-EILAAVPKRSRKTWAILLPeatvLGVRGDTLVLGF 552
                          170
                   ....*....|
gi 1907156703 3079 VSGNnvLAHR 3088
Cdd:PRK07764   553 STGG--LARR 560
RRM3_hnRNPQ cd12495
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q ...
121-184 1.31e-03

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 409918 [Multi-domain]  Cd Length: 72  Bit Score: 39.97  E-value: 1.31e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907156703  121 LSSNVSDQYLTRHFCRYGPVVKVvfDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12495      9 LANTVTEEILEKAFSQFGKLERV--KKLKDYAFIHFDERDGAVKAMDEMNGKDLEGENIEIVFA 70
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
36-99 1.37e-03

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409884 [Multi-domain]  Cd Length: 78  Bit Score: 40.08  E-value: 1.37e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLG 99
Cdd:cd12450      1 TLFVGNLSWSATQDDLENFFSDCGEVVDVRIamdRDDGRSKGFGHVEFASAESAQKALEKSGQDLGG 67
RRM3_hnRNPQ cd12495
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q ...
35-109 1.39e-03

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 409918 [Multi-domain]  Cd Length: 72  Bit Score: 39.59  E-value: 1.39e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEIvdidiKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 109
Cdd:cd12495      2 KVLFVRNLANTVTEEILEKAFSQFGKL-----ERVKKLKDYAFIHFDERDGAVKAMDEMNGKDLEGENIEIVFAK 71
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
37-107 1.45e-03

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 39.81  E-value: 1.45e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF 107
Cdd:cd12399      1 LYVGNLPYSASEEQLKSLFGQFGAVFDVKLpmDRETKRPRgFGFVELQEEESAEKAIAKLDGTDFMGRTIRVNE 74
RRM2_TIA1_like cd12353
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and ...
37-114 1.51e-03

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409789 [Multi-domain]  Cd Length: 75  Bit Score: 39.68  E-value: 1.51e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK---VNGVPQYAFLQYCDIASVCKAIKKMDGEYLGnnrlklgfGKSMPT 113
Cdd:cd12353      2 IFVGDLSPEIETEDLKEAFAPFGEISDARVVKdtqTGKSKGYGFVSFVKKEDAENAIQGMNGQWLG--------GRNIRT 73

                   .
gi 1907156703  114 N 114
Cdd:cd12353     74 N 74
RRM_ist3_like cd12411
RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ...
37-104 1.57e-03

RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well.


Pssm-ID: 409845 [Multi-domain]  Cd Length: 89  Bit Score: 39.88  E-value: 1.57e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLK 104
Cdd:cd12411     12 IYIGGLPYELTEGDILCVFSQYGEIVDINLvrDKKTGKSKgFAFLAYEDQRSTILAVDNLNGIKLLGRTIR 82
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
120-184 1.62e-03

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409981 [Multi-domain]  Cd Length: 76  Bit Score: 39.47  E-value: 1.62e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  120 GLSSNVSDQYLTRHFCRYGPV--VKVVFDRL---KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12565      7 NLPKYVTEKRLKEHFSKKGEItdVKVMRTKDgksRRFGFIGFKSEEEAQKAVKYFNKTFIDTSKISVEFA 76
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
1214-1449 1.68e-03

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 44.15  E-value: 1.68e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1214 TKEPEPKAPVSAGLPA-VTVTVVTPEPASSAPEKAEEAAEAPSPageKPAEPAPVSEETKLVSEPASVP----VEQPRQS 1288
Cdd:PLN03209   325 SQRVPPKESDAADGPKpVPTKPVTPEAPSPPIEEEPPQPKAVVP---RPLSPYTAYEDLKPPTSPIPTPpsssPASSKSV 401
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1289 DVPPGEDSRDSQDSAALAPSAPQESAATdaVPCVNAEPLTPGTTVSQVESsvdpkPSSPQPLSKLTQRSEEAEEGKVEK- 1367
Cdd:PLN03209   402 DAVAKPAEPDVVPSPGSASNVPEVEPAQ--VEAKKTRPLSPYARYEDLKP-----PTSPSPTAPTGVSPSVSSTSSVPAv 474
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1368 PDTTPSTEpdATQNAGVASEAQPPASEDV---EANPPVAAKDRKTNKSKRSKTSVQAAAASVVEKPVTRKSERIDREKLK 1444
Cdd:PLN03209   475 PDTAPATA--ATDAAAPPPANMRPLSPYAvydDLKPPTSPSPAAPVGKVAPSSTNEVVKVGNSAPPTALADEQHHAQPKP 552

                   ....*
gi 1907156703 1445 RSSSP 1449
Cdd:PLN03209   553 RPLSP 557
RRM1_Mug28 cd21620
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated ...
35-105 1.74e-03

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410199 [Multi-domain]  Cd Length: 84  Bit Score: 39.80  E-value: 1.74e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KK-----VNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 105
Cdd:cd21620      2 RSLYVGNLPQTCQSEDLIILFEPYGNVCGAHIasrKKvkvswVKPSKLFAFVEFETKEAATTAIVLLNGITYMGCQLKV 80
RRM_RBM42 cd12383
RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This ...
121-181 1.74e-03

RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409817 [Multi-domain]  Cd Length: 83  Bit Score: 39.57  E-value: 1.74e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703  121 LSSNVSDQYLTRHFCRYGPV--VKVVFDRL----KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 181
Cdd:cd12383     14 LGNEVTDEVLARAFSKYPSFqkAKVIRDKRtgksKGYGFVSFKDPNDYLKALREMNGKYVGNRPIKL 80
RRM_DNAJC17 cd12429
RNA recognition motif (RRM) found in the DnaJ homolog subfamily C member 17; The CD ...
126-171 1.78e-03

RNA recognition motif (RRM) found in the DnaJ homolog subfamily C member 17; The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding.


Pssm-ID: 409863 [Multi-domain]  Cd Length: 74  Bit Score: 39.56  E-value: 1.78e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1907156703  126 SDQYLTRHFCRYGPVVKVVF-DRLKGMALVLYSEIEDAQAAVKETKG 171
Cdd:cd12429     17 SEEELRKIFSKYGPVSDVVIsSKKKGSAIVEFATVVAADAAVENEVG 63
RRM1_Hrp1p cd12577
RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
37-102 1.93e-03

RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409991 [Multi-domain]  Cd Length: 76  Bit Score: 39.40  E-value: 1.93e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQ---YAFLQYCDIASVCKAIKK---MDGEYLGNNR 102
Cdd:cd12577      1 MFIGGLNWDTTEEGLRDYFSQFGTVVDCTIMKDSATGRsrgFGFLTFEDPSSVNEVMKKehvLDGKIIDPKR 72
RRM2_FCA cd12637
RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar ...
37-97 2.00e-03

RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain.


Pssm-ID: 410045 [Multi-domain]  Cd Length: 81  Bit Score: 39.67  E-value: 2.00e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQY---AFLQYCDIASVCKAIKKMDGEY 97
Cdd:cd12637      2 LFVGSLPKTATEQEVRDLFEAYGEVEEVYLMKDPVTQQGtgcAFVKFAYKEEALAAIRSLNGTV 65
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
37-113 2.14e-03

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 41.18  E-value: 2.14e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGKSMPT 113
Cdd:PLN03134    37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVivdRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPS 116
RRM_scw1_like cd12245
RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar ...
36-98 2.20e-03

RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar proteins; This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins.


Pssm-ID: 409691 [Multi-domain]  Cd Length: 79  Bit Score: 39.14  E-value: 2.20e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQyAFLQYCDIASVCKAIKKMDGEYL 98
Cdd:cd12245      4 TLFVANLGPNVSEQELRQLFSRQPGFRRLRMHNKGGGPV-CFVEFEDVPFATQALNHLQGAIL 65
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
113-181 2.24e-03

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 39.43  E-value: 2.24e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703  113 TNCVWLDGLSSNVSDQYLTRHFCRYGPVVKV--------VFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 181
Cdd:cd21619      1 SNTIYVGNIDMTINEDALEKIFSRYGQVESVrrppihtdKADRTTGFGFIKYTDAESAERAMQQADGILLGRRRLVV 77
RRM_hnRNPC_like cd12341
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C) ...
35-103 2.37e-03

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins; This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes.


Pssm-ID: 409778 [Multi-domain]  Cd Length: 68  Bit Score: 38.77  E-value: 2.37e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703   35 RTLFIGNLeKT--TTYHDLRNIFQRFGEIVDIDIKKvngvpQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 103
Cdd:cd12341      1 SRIFVGNL-PTdqMTKEDLEEIFSKYGKILGISLHK-----GYGFVQFDNEEDARAAVAGENGRTIKGQRL 65
RRM3_hnRNPR cd12494
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R ...
35-109 2.39e-03

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains.


Pssm-ID: 409917 [Multi-domain]  Cd Length: 72  Bit Score: 39.24  E-value: 2.39e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEIvdidiKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 109
Cdd:cd12494      2 KVLFVRNLATTVTEEILEKTFSQFGKL-----ERVKKLKDYAFVHFEDRDAAVKAMDEMNGKEVEGEEIEIVLAK 71
RRM_MCM3A_like cd12443
RNA recognition motif (RRM) found in 80 kDa MCM3-associated protein (Map80) and similar ...
128-174 2.40e-03

RNA recognition motif (RRM) found in 80 kDa MCM3-associated protein (Map80) and similar proteins; This subfamily corresponds to the RRM of Map80, also termed germinal center-associated nuclear protein (GANP), involved in the nuclear localization pathway of MCM3, a protein necessary for the initiation of DNA replication and also involves in controls that ensure DNA replication is initiated once per cell cycle. Map80 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409877 [Multi-domain]  Cd Length: 75  Bit Score: 39.22  E-value: 2.40e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1907156703  128 QYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKetKGRKI 174
Cdd:cd12443     16 EILRRHFSKFGKVARVFCNPRKNLAIVHFKDHESAALAKK--KGKLL 60
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
2871-3048 2.41e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 43.82  E-value: 2.41e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2871 PVASSISLASRTKTSAQVPPEGEPLQSTQSAQPAPSTQATQPIPPAPPCQPSQLSQPAQPPSGKIPQVSQEAKGTQTGGV 2950
Cdd:PRK07764   592 PGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPA 671
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2951 EQTrlPAIPTNRPSEPHAQLQRAPVETAQP-AHPSPVSVSMKPDLPSPLSSQAAPKQPLFVPANSGPSTPPGLALPHAEV 3029
Cdd:PRK07764   672 KAG--GAAPAAPPPAPAPAAPAAPAGAAPAqPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPP 749
                          170
                   ....*....|....*....
gi 1907156703 3030 QPAPKQESSPHGTPQRPVD 3048
Cdd:PRK07764   750 DPAGAPAQPPPPPAPAPAA 768
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
1193-1584 2.41e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 44.01  E-value: 2.41e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1193 KEAEKQEEPETHPkTPEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAGEKPAEPAPVSEETK 1272
Cdd:PHA03307    59 AAACDRFEPPTGP-PPGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPASPPPSPAPDLSEM 137
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1273 LVSEPASVPVeqPRQSDVPPGEDSRDSqdsAALAPSAPQESAATDAVPCVNAEPLTPGTTVSQVESSVDPKPSSPQPLSK 1352
Cdd:PHA03307   138 LRPVGSPGPP--PAASPPAAGASPAAV---ASDAASSRQAALPLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSP 212
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1353 LTQRSeeaeegkvekPDTTPSTEPDATQNAGVASEAQPPASEDVEANPPVAAKDRKTNKSKRSKTSVQAAAASVVE--KP 1430
Cdd:PHA03307   213 ISASA----------SSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPssRP 282
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1431 VTRKSERIDREKLKRSSSPRGEAqkllelkmEAEKITRTASKSSGGDTEHPEPSlPLSRSRRRNVRSVYATMTDHESRSP 1510
Cdd:PHA03307   283 GPASSSSSPRERSPSPSPSSPGS--------GPAPSSPRASSSSSSSRESSSSS-TSSSSESSRGAAVSPGPSPSRSPSP 353
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703 1511 AK-EPVEQPRVTRKRlerelQEAVVPPTTPRRGRPPKTRRRAEEDgEHERKEPAETPRPAEGWRSPRSQKSAAAA 1584
Cdd:PHA03307   354 SRpPPPADPSSPRKR-----PRPSRAPSSPAASAGRPTRRRARAA-VAGRARRRDATGRFPAGRPRPSPLDAGAA 422
RRM2_CoAA cd12609
RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator ...
116-182 2.45e-03

RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410021 [Multi-domain]  Cd Length: 68  Bit Score: 39.06  E-value: 2.45e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYGPVVKVvfDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVD 182
Cdd:cd12609      3 IFVGNVSATCTSDELRGLFEEFGRVVEC--DKVKDYAFVHMEREEEALAAIEALNGKEVKGRRINVE 67
RRM_PPARGC1A_like cd12357
RNA recognition motif (RRM) found in the peroxisome proliferator-activated receptor gamma ...
35-80 2.45e-03

RNA recognition motif (RRM) found in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators; This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing.


Pssm-ID: 409793 [Multi-domain]  Cd Length: 91  Bit Score: 39.72  E-value: 2.45e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQY 80
Cdd:cd12357      3 RVVYVGKLEQDTTRSELRRRFEVFGEIEECTVHFRERGDKYGFVTY 48
RRM1_RBM19 cd12564
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
37-103 2.45e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409980 [Multi-domain]  Cd Length: 76  Bit Score: 39.22  E-value: 2.45e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIK--KVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 103
Cdd:cd12564      3 LIVKNLPSSITEDRLRKLFSAFGTITDVQLKytKDGKFRRFGFVGFKSEEEAQKALKHFNNSFIDTSRI 71
RRM1_TIA1_like cd12352
RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and ...
37-104 2.54e-03

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409788 [Multi-domain]  Cd Length: 73  Bit Score: 38.93  E-value: 2.54e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVPqYAFLQYCDIASVCKAIKKMDGEYLGNNRLK 104
Cdd:cd12352      1 LYVGNLDRQVTEDLILQLFSQIGPCKSCKMitEHGGNDP-YCFVEFYEHNHAAAALQAMNGRKILGKEVK 69
RRM1_PSP1 cd12586
RNA recognition motif 1 (RRM1) found in vertebrate paraspeckle protein 1 (PSP1); This subgroup ...
37-107 2.59e-03

RNA recognition motif 1 (RRM1) found in vertebrate paraspeckle protein 1 (PSP1); This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 409999 [Multi-domain]  Cd Length: 71  Bit Score: 38.75  E-value: 2.59e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGvpqYAF--LQYCDIASVCKAikKMDGEYLGNNRLKLGF 107
Cdd:cd12586      4 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRG---FGFirLESRTLAEIAKA--ELDGTILKSRPLRIRF 71
RRM1_PUB1 cd12614
RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated ...
37-105 2.68e-03

RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410026 [Multi-domain]  Cd Length: 74  Bit Score: 38.95  E-value: 2.68e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEI--VDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 105
Cdd:cd12614      1 LYVGNLDPRVTEDLLQEIFAVTGPVenCKIIPDKNSKGVNYGFVEYYDRRSAEIAIQTLNGRQIFGQEIKV 71
PHA03247 PHA03247
large tegument protein UL36; Provisional
1261-1846 2.89e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.77  E-value: 2.89e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1261 PAEPAPvseeTKLVSEPASVPVeQPRQSDVPPGED---SRDSQDSAALAPSAPQESAATDAVPCVNAEPLTPGTTVSQVE 1337
Cdd:PHA03247  2512 PSRLAP----AILPDEPVGEPV-HPRMLTWIRGLEelaSDDAGDPPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAVTSRA 2586
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1338 SSVDPKPSSPQPlskltqRSEEAEEGKVEKPDTTPSTEPDATQNAGVASEAQPPASEDVEANPPVAAKDRKTNKskrskt 1417
Cdd:PHA03247  2587 RRPDAPPQSARP------RAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRD------ 2654
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1418 svqAAAASVVEKPvtRKSERIDREKlKRSSSPRGEAQKllELKMEAEKITRTASKSSGGDTEHPEP-----SLPLSRSRR 1492
Cdd:PHA03247  2655 ---DPAPGRVSRP--RRARRLGRAA-QASSPPQRPRRR--AARPTVGSLTSLADPPPPPPTPEPAPhalvsATPLPPGPA 2726
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1493 RNVRSVYATMTDHESRSPAKEPVeQPRVTRKRLERELQEAVVPPTTPR--RGRPPKTRRRAEEDGEHERKEPAETPRPAE 1570
Cdd:PHA03247  2727 AARQASPALPAAPAPPAVPAGPA-TPGGPARPARPPTTAGPPAPAPPAapAAGPPRRLTRPAVASLSESRESLPSPWDPA 2805
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1571 GWRSPRSQKSAAAAGPQGKRGRNEQKVEAAAEAGAQASTREGNPKSRGEREAASEPKRdRRDPStdkngpdtfpvevleR 1650
Cdd:PHA03247  2806 DPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVR-RRPPS---------------R 2869
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1651 KPPEKTYKSKRGRARStrsaMDRAAHQRSLEMAARAAGQAADKEAGPAAASPQESESPQKGSGSSPQLaNNPADPDREAE 1730
Cdd:PHA03247  2870 SPAAKPAAPARPPVRR----LARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPP-PPPPRPQPPLA 2944
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1731 EESASASTAPPEGTQLARQIEL-----EQAVQNIAKLPEPSAAAASKGT--------------ATATAASEE--PAPEHG 1789
Cdd:PHA03247  2945 PTTDPAGAGEPSGAVPQPWLGAlvpgrVAVPRFRVPQPAPSREAPASSTppltghslsrvsswASSLALHEEtdPPPVSL 3024
                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703 1790 HKPAHQASETELAAAIGSIISDAsgEPENFSAPPSVPPGSQTHPREGMEPGLHEAES 1846
Cdd:PHA03247  3025 KQTLWPPDDTEDSDADSLFDSDS--ERSDLEALDPLPPEPHDPFAHEPDPATPEAGA 3079
RRM2_TDP43 cd12322
RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar ...
35-68 2.99e-03

RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins; This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity.


Pssm-ID: 409761 [Multi-domain]  Cd Length: 71  Bit Score: 38.84  E-value: 2.99e-03
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK 68
Cdd:cd12322      1 RKVFVGRCTEDMTEDDLRQYFSQFGEVTDVFIPK 34
RRM1_p54nrb_like cd12332
RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
37-107 3.01e-03

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409769 [Multi-domain]  Cd Length: 71  Bit Score: 38.82  E-value: 3.01e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF 107
Cdd:cd12332      4 LFVGNLPNDITEEEFKELFQKYGEVSEVFLNKGKG---FGFIRLDTRANAEAAKAELDGTPRKGRQLRVRF 71
RRM1_LARP7 cd12290
RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; ...
36-93 3.06e-03

RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus.


Pssm-ID: 409732 [Multi-domain]  Cd Length: 79  Bit Score: 38.85  E-value: 3.06e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKM 93
Cdd:cd12290      1 TVYVELLPKNATHEWIEAVFSKYGEVVYVSIpryKSTGDPKGFAFIEFETSESAQKAVKHF 61
RRM1_PTBP1_hnRNPL_like cd12421
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
120-186 3.24e-03

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM.


Pssm-ID: 409855 [Multi-domain]  Cd Length: 74  Bit Score: 38.71  E-value: 3.24e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703  120 GLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVK--ETKGRKIGGNKIKVDFANR 186
Cdd:cd12421      6 NLPPDATEADLVALGLPFGKVTNVLLLKGKNQALVEMEDVESASSMVNyyTTVPPLIRGRPVYVQYSNH 74
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
34-107 3.24e-03

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409981 [Multi-domain]  Cd Length: 76  Bit Score: 38.70  E-value: 3.24e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907156703   34 TRtLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVP-QYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF 107
Cdd:cd12565      1 SR-IIVKNLPKYVTEKRLKEHFSKKGEITDVKVmRTKDGKSrRFGFIGFKSEEEAQKAVKYFNKTFIDTSKISVEF 75
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
1188-1416 3.34e-03

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 42.99  E-value: 3.34e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1188 KDQKPKEAEKQEEPE------THPKTPEPAAETKEPEPKAPVSAGLPAVTVTV-----VTPEPASSAPEKAEEAAEAPSP 1256
Cdd:PLN03209   326 QRVPPKESDAADGPKpvptkpVTPEAPSPPIEEEPPQPKAVVPRPLSPYTAYEdlkppTSPIPTPPSSSPASSKSVDAVA 405
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1257 AGEKPaEPAPVSEETKLVSEPASVPVEQPRQSDVPPGEDSRDSQDSAALAPSAPQESAATDAVPcvNAEPLTPGT-TVSQ 1335
Cdd:PLN03209   406 KPAEP-DVVPSPGSASNVPEVEPAQVEAKKTRPLSPYARYEDLKPPTSPSPTAPTGVSPSVSST--SSVPAVPDTaPATA 482
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1336 VESSVDPKPSSPQPLSKLTQRSEeaeegkvEKPDTTPSTepdATQNAGVASEAQPPASEDVEANPPVAAKDRKTNKSKRS 1415
Cdd:PLN03209   483 ATDAAAPPPANMRPLSPYAVYDD-------LKPPTSPSP---AAPVGKVAPSSTNEVVKVGNSAPPTALADEQHHAQPKP 552

                   .
gi 1907156703 1416 K 1416
Cdd:PLN03209   553 R 553
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
119-181 3.46e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.


Pssm-ID: 409751 [Multi-domain]  Cd Length: 73  Bit Score: 38.40  E-value: 3.46e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703  119 DGLSSNVSDQYLTRHFCRYGPVVKVVFDR------LKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 181
Cdd:cd12311      4 DNLTYRTTPDDLRRVFEKYGEVGDVYIPRdrytreSRGFAFVRFYDKRDAEDAIDAMDGAELDGRELRV 72
PHA03247 PHA03247
large tegument protein UL36; Provisional
2551-3052 3.57e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.39  E-value: 3.57e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2551 PSTPADRTIAHLATPKPDTHSPRPTGPTPglfPRPCHPSsttstalstnatvmlAAGIPVPQFISSIHPEQSVimPPHSI 2630
Cdd:PHA03247  2475 PGAPVYRRPAEARFPFAAGAAPDPGGGGP---PDPDAPP---------------APSRLAPAILPDEPVGEPV--HPRML 2534
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2631 TQTVSLGHLSQGEVRMSTPTLPSITYSIRPE-TLHSPRAPLQPQQ--IEARAPQRVGTPQPATTGVPALATQHPPEEEVH 2707
Cdd:PHA03247  2535 TWIRGLEELASDDAGDPPPPLPPAAPPAAPDrSVPPPRPAPRPSEpaVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPP 2614
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2708 YHLPVARAA--APVQSEVLVMQSEYRLHPYTVPRDVRIMVHPHVTAVSeQPRATEGVVKVPPANKAPQQLVKEAVKTSDA 2785
Cdd:PHA03247  2615 SPLPPDTHApdPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVS-RPRRARRLGRAAQASSPPQRPRRRAARPTVG 2693
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2786 KAVPAPAPVPVPVPVPTPAPPPhGEARILTVTPSSQLQGLPLT-----PPVVVTHGVQIVHSSGELFQEYRYGDVRTYHA 2860
Cdd:PHA03247  2694 SLTSLADPPPPPPTPEPAPHAL-VSATPLPPGPAAARQASPALpaapaPPAVPAGPATPGGPARPARPPTTAGPPAPAPP 2772
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2861 PAQQLTHTQFPVASSISLASRTKTSAQVPPEGEPLQSTQSAQPAPSTQATQPIPPAPPCQPSQLSQPAqPPSGKIPQVSQ 2940
Cdd:PHA03247  2773 AAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPP-PPPGPPPPSLP 2851
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2941 EAKGTQTGGVEQTRLP-----AIPTNRPSEPHAQLQRAPVEtaqpahPSPVSVSMKPDLPSPLSSQAAPKQPLFVPANSG 3015
Cdd:PHA03247  2852 LGGSVAPGGDVRRRPPsrspaAKPAAPARPPVRRLARPAVS------RSTESFALPPDQPERPPQPQAPPPPQPQPQPPP 2925
                          490       500       510
                   ....*....|....*....|....*....|....*....
gi 1907156703 3016 PS--TPPGLALPHAEVQPAPKQESSPHGTPQRPVDMVQL 3052
Cdd:PHA03247  2926 PPqpQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWL 2964
RRM2_EAR1_like cd12527
RNA recognition motif 2 (RRM2) found in terminal EAR1-like proteins; This subgroup corresponds ...
36-103 3.74e-03

RNA recognition motif 2 (RRM2) found in terminal EAR1-like proteins; This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins.


Pssm-ID: 409947 [Multi-domain]  Cd Length: 71  Bit Score: 38.29  E-value: 3.74e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVdiDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 103
Cdd:cd12527      3 SLVILNLLPAVSSFTLREIFQVYGDVK--DVRETPLKPSQRFVEFFDVRDAARALHEMNGKEIFGKRL 68
PHA03247 PHA03247
large tegument protein UL36; Provisional
1535-2157 3.75e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.39  E-value: 3.75e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1535 PPTTPRRGRPPKTRRRAEEdgeherKEPAETP-RPAEGWRSPRSQKSAAAAGPQGKRGRNEQKVEAAAEAGAQASTREGN 1613
Cdd:PHA03247  2552 PPPLPPAAPPAAPDRSVPP------PRPAPRPsEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPD 2625
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1614 PKSRGEREAASEPKRDRRDPSTDKNGPDTFPVEVLERKPPEKTYKSKRGRARSTRSAMDRAAHQR---SLEMAARAAGQA 1690
Cdd:PHA03247  2626 PPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPtvgSLTSLADPPPPP 2705
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1691 ADKEAGPAAASPQE--SESPQKGSGSSPQLANNPADPdreaeeesasastAPPEGtqlarqieleqavqniaklPEPSAA 1768
Cdd:PHA03247  2706 PTPEPAPHALVSATplPPGPAAARQASPALPAAPAPP-------------AVPAG-------------------PATPGG 2753
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1769 AASKGTATATAASEEPAPEHGHKPAHQASETELAAAIGSIISDASGEPENFSAPPSVPPGSQTHPREGMEPGlheaesgi 1848
Cdd:PHA03247  2754 PARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPA-------- 2825
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1849 leTGTATESSAPQVSALDPPEGSADTKETRGNSgdsvqeAKGSKVEVTPPRKdkgrqkttrrrkrNANKKVVAITETRAS 1928
Cdd:PHA03247  2826 --GPLPPPTSAQPTAPPPPPGPPPPSLPLGGSV------APGGDVRRRPPSR-------------SPAAKPAAPARPPVR 2884
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1929 EAEQTQsespaaeeataatpEAPQEEKQSEKPPSPPaectfdPSKTPPAESLSQENSAAEKTPCKAPvlpalpPLSQPAL 2008
Cdd:PHA03247  2885 RLARPA--------------VSRSTESFALPPDQPE------RPPQPQAPPPPQPQPQPPPPPQPQP------PPPPPPR 2938
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2009 MDDGPQARFKVHSIIESDPVTPPSDSGIPPPTIPLVTIAKLPPPVIPGGVPHQSPPPKvtewiTRQEEPRAQS-TPSPAL 2087
Cdd:PHA03247  2939 PQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPL-----TGHSLSRVSSwASSLAL 3013
                          570       580       590       600       610       620       630
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703 2088 PPDTkasdmDTSSSTLRKILMDPKyvSATGVTSTSVTSAIAEPVSAPCLQEAPAPPCDP-KHPPLEGVSAA 2157
Cdd:PHA03247  3014 HEET-----DPPPVSLKQTLWPPD--DTEDSDADSLFDSDSERSDLEALDPLPPEPHDPfAHEPDPATPEA 3077
RRM2_MEI2_EAR1_like cd12276
RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; ...
116-181 3.85e-03

RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 409718 [Multi-domain]  Cd Length: 71  Bit Score: 38.39  E-value: 3.85e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKG-MALVLYSEIEDAQAAVKETKGRKIGGNKIKV 181
Cdd:cd12276      4 LLVFNLDAPVSNDELKSLFSKFGEIKEIRPTPDKPsQKFVEFYDVRDAEAALDGLNGRELLGGKLKV 70
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
1192-1349 3.86e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 42.91  E-value: 3.86e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1192 PKEAEKQEEPETHPKTPEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAGEKPAEPAPVSEET 1271
Cdd:PRK07003   385 ARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADSRCD 464
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703 1272 KLVSEPASvpveQPRQSDVPPGedsrDSQDSAALAPSAPQ-ESAATDAVPCVNAEPLTPGTTVSQVESSVDPKPSSPQP 1349
Cdd:PRK07003   465 ERDAQPPA----DSGSASAPAS----DAPPDAAFEPAPRAaAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPP 535
RRM_SRSF10_SRSF12 cd12312
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and ...
130-184 3.93e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 240758 [Multi-domain]  Cd Length: 84  Bit Score: 38.89  E-value: 3.93e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703  130 LTRHFCRYGPVVKVVFD------RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12312     17 LRREFGRYGPIVDVYIPldfytrRPRGFAYIQFEDVRDAEDALYYLDRTRFLGREIEIQFA 77
RRM1_Hu_like cd12375
RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
121-184 4.09e-03

RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 409810 [Multi-domain]  Cd Length: 76  Bit Score: 38.54  E-value: 4.09e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703  121 LSSNVSDQYLTRHFCRYGPV--VKVVFDRLKGMAL----VLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12375      7 LPQSMTQEELRSLFGAIGPIesCKLVRDKITGQSLgygfVNYRDPNDARKAINTLNGLDLENKRLKVSYA 76
RRM_ENOX cd12228
RNA recognition motif (RRM) found in the cell surface Ecto-NOX disulfide-thiol exchanger ...
31-106 4.14e-03

RNA recognition motif (RRM) found in the cell surface Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX) proteins; This subgroup corresponds to the conserved RNA recognition motif (RRM) in ECTO-NOX proteins (also termed ENOX), comprising a family of plant and animal NAD(P)H oxidases exhibiting both, oxidative and protein disulfide isomerase-like, activities. They are growth-related and drive cell enlargement, and may play roles in aging and neurodegenerative diseases. ENOX proteins function as terminal oxidases of plasma membrane electron transport (PMET) through catalyzing electron transport from plasma membrane quinones to extracellular oxygen, forming water as a product. They are also hydroquinone oxidases that oxidize externally supplied NADH, hence NOX. ENOX proteins harbor a di-copper center that lack flavin. ENOX proteins display protein disulfide interchange activity that is also possessed by protein disulfide isomerase. In contrast to the classic protein disulfide isomerases, ENOX proteins lack the double CXXC motif. This family includes two ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed candidate growth-related and time keeping constitutive hydroquinone [NADH] oxidase (cCNOX), or cell proliferation-inducing gene 38 protein, or Constitutive Ecto-NOX (cNOX), is the constitutively expressed cell surface NADH (ubiquinone) oxidase that is ubiquitous and refractory to drugs. ENOX2, also termed APK1 antigen, or cytosolic ovarian carcinoma antigen 1, or tumor-associated hydroquinone oxidase (tNOX), is a cancer-specific variant of ENOX1 and plays a key role in cell proliferation and tumor progression. In contrast to ENOX1, ENOX2 is drug-responsive and harbors a drug binding site to which the cancer-specific S-peptide tagged pan-ENOX2 recombinant (scFv) is directed. Moreover, ENOX2 is specifically inhibited by a variety of quinone site inhibitors that have anticancer activity and is unique to the surface of cancer cells. ENOX proteins contain many functional motifs.


Pssm-ID: 409675 [Multi-domain]  Cd Length: 84  Bit Score: 38.56  E-value: 4.14e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907156703   31 PKATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNgvpqYAFLQYCDIASVCKAIkkmdgeYLGNNRLKLG 106
Cdd:cd12228      3 PPGCKTVFVGGLPENATEEIIREVFEQCGEIIAIRMSKKN----FCHIRFAEEFAVDKAI------YLSGYRVRLG 68
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
37-103 4.15e-03

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 38.15  E-value: 4.15e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRL 103
Cdd:cd12340      2 LFVRPFPPDTSESAIREIFSPYGPVKEVKMLSDSN---FAFVEFEELEDAIRAKDSVHGRVLNNEPL 65
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
36-104 4.33e-03

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.


Pssm-ID: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 38.42  E-value: 4.33e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI------KKVNGVpqyAFLQYCDIASVCKAIKKMDGEYLGNNRLK 104
Cdd:cd12393      3 TVYVSNLPFSLTNNDLHQIFSKYGKVVKVTIlkdketRKSKGV---AFVLFLDRESAHNAVRAMNNKELFGRTLK 74
RRM2_CELF3_4_5_6 cd12635
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
35-95 4.36e-03

RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.


Pssm-ID: 410043 [Multi-domain]  Cd Length: 81  Bit Score: 38.55  E-value: 4.36e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDG 95
Cdd:cd12635      2 RKLFVGMLGKQQSEDDVRRLFEPFGSIEECTIlRGPDGNSKgCAFVKFSSHAEAQAAINALHG 64
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
2370-2701 4.48e-03

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 42.98  E-value: 4.48e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2370 TEGPQRISAKISQIPPASAmdiefqqsVSKSQVKADSITPTQSAPkgpqTPSAfanvaahstlvlTAQTYNASPVISSVK 2449
Cdd:pfam05109  529 TPTPNATSPTLGKTSPTSA--------VTTPTPNATSPTPAVTTP----TPNA------------TIPTLGKTSPTSAVT 584
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2450 TDRPSLEKPepihlSVSTPVTQGGTVKVLTQGINTPPVLVHNQLVLTPSIVTTNKKLADPVTLKIEtkvLQPANLGPTLT 2529
Cdd:pfam05109  585 TPTPNATSP-----TVGETSPQANTTNHTLGGTSSTPVVTSPPKNATSAVTTGQHNITSSSTSSMS---LRPSSISETLS 656
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2530 PHHPPALPSKLPAEVNHVPSGPSTPADRTIAHLATPKPDTHSPrptGPTPGLFPRPCHPSSTTSTALSTNATVmlAAGIP 2609
Cdd:pfam05109  657 PSTSDNSTSHMPLLTSAHPTGGENITQVTPASTSTHHVSTSSP---APRPGTTSQASGPGNSSTSTKPGEVNV--TKGTP 731
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2610 VPQFISSIHPE-QSVIMPPHSIT-----QTVSLGHLSQGEVRMST-PTLPSITYSIRPETLHSPRAPLQPQQIEARAPQR 2682
Cdd:pfam05109  732 PKNATSPQAPSgQKTAVPTVTSTggkanSTTGGKHTTGHGARTSTePTTDYGGDSTTPRTRYNATTYLPPSTSSKLRPRW 811
                          330       340
                   ....*....|....*....|..
gi 1907156703 2683 VGTPQPATTG---VPALATQHP 2701
Cdd:pfam05109  812 TFTSPPVTTAqatVPVPPTSQP 833
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
38-99 4.54e-03

RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only.


Pssm-ID: 409747 [Multi-domain]  Cd Length: 73  Bit Score: 38.44  E-value: 4.54e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703   38 FIGNLEKTTTYHDLRNIFQRFGEIVDIDIK--KVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLG 99
Cdd:cd12306      3 YVGNVDYGTTPEELQAHFKSCGTINRVTILcdKFTGQPKgFAYIEFVDKSSVENALLLNESEFRG 67
RRM2_RBM4 cd12607
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup ...
37-103 4.65e-03

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4.


Pssm-ID: 410019 [Multi-domain]  Cd Length: 67  Bit Score: 38.02  E-value: 4.65e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIkkvngVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 103
Cdd:cd12607      3 LHVGNISSSCTNQELRAKFEEYGPVIECDI-----VKDYAFVHMERAEDAMEAIRGLDNTEFQGKRM 64
RRM1_SRSF4_like cd12337
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and ...
37-109 4.82e-03

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 409774 [Multi-domain]  Cd Length: 70  Bit Score: 38.07  E-value: 4.82e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKkvNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 109
Cdd:cd12337      2 VYIGRLPYRARERDVERFFRGYGRIRDINLK--NG---FGFVEFEDPRDADDAVYELNGKELCGERVIVEHAR 69
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
116-184 4.97e-03

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 38.15  E-value: 4.97e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907156703  116 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 184
Cdd:cd12262      6 VYVGNLDDSLTEEEIRGILEKYGEIESIKILKEKNCAFVNYLNIANAIKAVQELPIKNPKFKKVRINYG 74
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
1754-2180 5.06e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 42.67  E-value: 5.06e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1754 QAVQNIAKLPEPSAAAASKGTATATAASEEPAPEHGHKPAHQASETELAAAIGSiisDASGEPENFSAPPSVPPGSQThP 1833
Cdd:PRK07764   403 AAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSP---PPAAAPSAQPAPAPAAAPEPT-A 478
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1834 REGMEPGLHEAESGILETGTATESSAPQVSALDPPEGSADTKETRGNSGDSVQEAKGSKVEVTPPRKD-------KGRQK 1906
Cdd:PRK07764   479 APAPAPPAAPAPAAAPAAPAAPAAPAGADDAATLRERWPEILAAVPKRSRKTWAILLPEATVLGVRGDtlvlgfsTGGLA 558
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1907 TTRRRKRNANKKVVAITE----TRASEAEQTQSESPAAEEATAATPEAPQEEKQSEkPPSPPAECTFDPSKTPPAESLSQ 1982
Cdd:PRK07764   559 RRFASPGNAEVLVTALAEelggDWQVEAVVGPAPGAAGGEGPPAPASSGPPEEAAR-PAAPAAPAAPAAPAPAGAAAAPA 637
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1983 ENSAAEKTPCKAPVLPALPPLSQPALMDDGPQARFKVHSIIESDPVTPPSDSGIPPPTIPlvtiaklpppvipggVPHQS 2062
Cdd:PRK07764   638 EASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAA---------------PAQPA 702
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 2063 PPPkvtewitRQEEPRAQSTPSPALPPDTKASDMDTSSSTLRKILMDPkyvsatgvtstsvtsaiaEPVSAPCLQEAPAP 2142
Cdd:PRK07764   703 PAP-------AATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPP------------------EPDDPPDPAGAPAQ 757
                          410       420       430
                   ....*....|....*....|....*....|....*...
gi 1907156703 2143 PCDPKHPPLEGVSAAAVPNADTQASEVPVAADKEKVAP 2180
Cdd:PRK07764   758 PPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDD 795
RRM1_MEI2_fungi cd12525
RNA recognition motif 1 (RRM1) found in fungal Mei2-like proteins; This subgroup corresponds ...
33-77 5.56e-03

RNA recognition motif 1 (RRM1) found in fungal Mei2-like proteins; This subgroup corresponds to the RRM1 of fungal Mei2-like proteins. The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif.


Pssm-ID: 409945 [Multi-domain]  Cd Length: 91  Bit Score: 38.53  E-value: 5.56e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1907156703   33 ATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKV--NGVPQYAF 77
Cdd:cd12525      6 PTRYLKVTGVPKDVSTSNLKEIFEKMGDVKGIFVKKLlsKGIVIVSF 52
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
1205-1315 5.59e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 42.39  E-value: 5.59e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1205 PKTPEPAAETKEPEPkAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAGEKPAEPAPVSEetkLVSEPASVPVEQ 1284
Cdd:PRK14951   381 PARPEAAAPAAAPVA-QAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPAA---VALAPAPPAQAA 456
                           90       100       110
                   ....*....|....*....|....*....|.
gi 1907156703 1285 PRQSDVPPGEDSRDSQDSAALAPSAPQESAA 1315
Cdd:PRK14951   457 PETVAIPVRVAPEPAVASAAPAPAAAPAAAR 487
PRK08691 PRK08691
DNA polymerase III subunits gamma and tau; Validated
1185-1390 5.60e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236333 [Multi-domain]  Cd Length: 709  Bit Score: 42.39  E-value: 5.60e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1185 EKEKDQKPKEAEKQEEPETHPKTPEPAAETKEPEPKAPVSAGLPAVTVTVvtpEPASSAPEKAEEAAEAPSPAGEKPAEP 1264
Cdd:PRK08691   373 ENTELQSPSAQTAEKETAAKKPQPRPEAETAQTPVQTASAAAMPSEGKTA---GPVSNQENNDVPPWEDAPDEAQTAAGT 449
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1265 APVSEET-KLVSEPASVPVEQPRQSDVPPGEdsrdsqdSAALAPSAPQESAATdAVPcvNAEPLtpgttvsQVESSVDPK 1343
Cdd:PRK08691   450 AQTSAKSiQTASEAETPPENQVSKNKAADNE-------TDAPLSEVPSENPIQ-ATP--NDEAV-------ETETFAHEA 512
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 1907156703 1344 PSSPQPLSKLTQRSEEAEEGKVEKPDTTPSTEPDATQNAGVASEAQP 1390
Cdd:PRK08691   513 PAEPFYGYGFPDNDCPPEDGAEIPPPDWEHAAPADTAGGGADEEAEA 559
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
37-99 5.62e-03

RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.


Pssm-ID: 409783 [Multi-domain]  Cd Length: 75  Bit Score: 37.97  E-value: 5.62e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI------KKVNGvpqYAFLQYCDIASVCKAIKKMD-GEYLG 99
Cdd:cd12347      1 LYVGGLAEEVDEKVLHAAFIPFGDIVDIQIpldyetEKHRG---FAFVEFEEAEDAAAAIDNMNeSELFG 67
RRM1_RBM45 cd12366
RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; ...
44-100 5.66e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409801 [Multi-domain]  Cd Length: 81  Bit Score: 38.07  E-value: 5.66e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703   44 KTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGN 100
Cdd:cd12366     12 KSVTEDDLREAFSPFGEIQDIWVvkdKQTKESKGIAYVKFAKSSQAARAMEEMHGKCLGD 71
RRM_RBM44 cd12248
RNA recognition motif (RRM) found in RNA-binding protein 44 (RBM44) and similar proteins; ...
120-181 5.74e-03

RNA recognition motif (RRM) found in RNA-binding protein 44 (RBM44) and similar proteins; This subgroup corresponds to the RRM of RBM44, a novel germ cell intercellular bridge protein that is localized in the cytoplasm and intercellular bridges from pachytene to secondary spermatocyte stages. RBM44 interacts with itself and testis-expressed gene 14 (TEX14). Unlike TEX14, RBM44 does not function in the formation of stable intercellular bridges. It carries an RNA recognition motif (RRM) that could potentially bind a multitude of RNA sequences in the cytoplasm and help to shuttle them through the intercellular bridge, facilitating their dispersion into the interconnected neighboring cells.


Pssm-ID: 409694 [Multi-domain]  Cd Length: 77  Bit Score: 37.97  E-value: 5.74e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703  120 GLSSNVSDQYLTRHFCRYGpVVKVVFDRLK---GMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 181
Cdd:cd12248      8 NLAPSVSEEDLLMHFEKYH-VSKISIQKLSmnyRYASLTFDDASDAQAAVKEMNGKDISGRKVKV 71
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
1198-1407 5.91e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 42.17  E-value: 5.91e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1198 QEEPETHPKTPEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAGEKPAEPAPVseetklvseP 1277
Cdd:PRK12323   384 QPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPA---------P 454
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1278 ASVPVEQPRQSDVPPGEDSRDSQDSAALAPSAPQESAATDAVPCVNAEPLTPGTtvsqvessvdPKPSSPQPLSKLTQRS 1357
Cdd:PRK12323   455 AAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPPPWEELPPEFAS----------PAPAQPDAAPAGWVAE 524
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1358 EEAEEGKVEKPDTTPSTEPDATqnAGVASEAQPPASEDVEANPPVAAKDR 1407
Cdd:PRK12323   525 SIPDPATADPDDAFETLAPAPA--AAPAPRAAAATEPVVAPRPPRASASG 572
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
36-106 6.03e-03

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 37.98  E-value: 6.03e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLG 106
Cdd:cd12412      4 RIFVGGIDWDTTEEELREFFSKFGKVKDVKIiKDRAGVSKgYGFVTFETQEDAEKIQKWGANLVFKGKKLNVG 76
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
35-109 6.56e-03

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 37.61  E-value: 6.56e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703   35 RTLFIGNLEKTTTYHDLRNIFQRFGEivdidIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 109
Cdd:cd12251      2 KVLYVRNLMLSTTEEKLRELFSEYGK-----VERVKKIKDYAFVHFEERDDAVKAMEEMNGKELEGSEIEVSLAK 71
PRK13108 PRK13108
prolipoprotein diacylglyceryl transferase; Reviewed
1739-1902 7.00e-03

prolipoprotein diacylglyceryl transferase; Reviewed


Pssm-ID: 237284 [Multi-domain]  Cd Length: 460  Bit Score: 41.89  E-value: 7.00e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1739 APPEGTQLARQIELEQAVQNIAKLPEPSAAAAskgtaTATAASEEPAPEHGHKPAHQASETELAAAIGSIISDASGEPEN 1818
Cdd:PRK13108   274 LAPKGREAPGALRGSEYVVDEALEREPAELAA-----AAVASAASAVGPVGPGEPNQPDDVAEAVKAEVAEVTDEVAAES 348
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1819 FSAPPSVPPGSQTHPREGMEPGLHEAESGILEtgtATESSAPQVSALDPPE--GSADTKETRGNSGDSVQEAKGSKVEVT 1896
Cdd:PRK13108   349 VVQVADRDGESTPAVEETSEADIEREQPGDLA---GQAPAAHQVDAEAASAapEEPAALASEAHDETEPEVPEKAAPIPD 425

                   ....*.
gi 1907156703 1897 PPRKDK 1902
Cdd:PRK13108   426 PAKPDE 431
RRM1_SNF cd12476
RNA recognition motif 1 (RRM1) found in Drosophila melanogaster sex determination protein SNF ...
32-95 7.26e-03

RNA recognition motif 1 (RRM1) found in Drosophila melanogaster sex determination protein SNF and similar proteins; This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently.


Pssm-ID: 409905 [Multi-domain]  Cd Length: 85  Bit Score: 37.97  E-value: 7.26e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907156703   32 KATRTLFIGNLEKTTTYHDLRN----IFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDG 95
Cdd:cd12476      4 RPNQTIYINNLNEKVKKEELKKslyaIFSQFGQILDIVALKTLKMRGQAFVIFKDISSATNALRSMQG 71
RRM1_RBM4 cd12606
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup ...
37-93 7.45e-03

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4.


Pssm-ID: 410018 [Multi-domain]  Cd Length: 67  Bit Score: 37.48  E-value: 7.45e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKvngvpQYAFLQYCDIASVCKAIKKM 93
Cdd:cd12606      3 LFIGNLPREATEEEIRSLFEQYGKVTECDIIK-----NYGFVHMEDKSAADEAIRNL 54
PHA03247 PHA03247
large tegument protein UL36; Provisional
1191-1409 7.52e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 42.23  E-value: 7.52e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1191 KPKEAEKQEEPETHPKT--------PEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEK---AEEAAEAPSPAGE 1259
Cdd:PHA03247  2700 DPPPPPPTPEPAPHALVsatplppgPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTagpPAPAPPAAPAAGP 2779
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1260 KPAEPAPVSEETKLVSEPASVPveqPRQSDVPPGEDSRDSQDSAALAPSAPqESAATDAVPCVNAEPLTPGTTVSQVESS 1339
Cdd:PHA03247  2780 PRRLTRPAVASLSESRESLPSP---WDPADPPAAVLAPAAALPPAASPAGP-LPPPTSAQPTAPPPPPGPPPPSLPLGGS 2855
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907156703 1340 VDP------KPSSPQPLSKLTQRSEEAEEgKVEKPDTTPSTEPDATQNAGVASEAQPPASEDVEANPPVAAKDRKT 1409
Cdd:PHA03247  2856 VAPggdvrrRPPSRSPAAKPAAPARPPVR-RLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQ 2930
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
1217-1445 7.93e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.90  E-value: 7.93e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1217 PEPKAPVSAGLPAVTVTV---VTPEPASSAPEKAEEAAEAPSPAGEkPAEPAPVSEETKLVSEPASVPVEQPRQSDVPPG 1293
Cdd:PRK07764   590 PAPGAAGGEGPPAPASSGppeEAARPAAPAAPAAPAAPAPAGAAAA-PAEASAAPAPGVAAPEHHPKHVAVPDASDGGDG 668
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1294 EDSRDSQDSAALAPSAPQESAATDAVPCVNAEPLTPGTTVSQVESSVDPKPSSPQPlskltqRSEEAEEGKVEKPDTTPS 1373
Cdd:PRK07764   669 WPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQA------AQGASAPSPAADDPVPLP 742
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907156703 1374 TEPDAtQNAGVASEAQPPASEDVEANPPVAAKDRKTNKSKRSKTSVQAAAAsvVEKPVTRKSERIDREKLKR 1445
Cdd:PRK07764   743 PEPDD-PPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPS--MDDEDRRDAEEVAMELLEE 811
RRM2_hnRNPA_like cd12328
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
37-90 7.98e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409766 [Multi-domain]  Cd Length: 73  Bit Score: 37.63  E-value: 7.98e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156703   37 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAI 90
Cdd:cd12328      2 LFVGGLKEDVEEEDLREYFSQFGKVESVEIvtdKETGKKRGFAFVTFDDHDSVDKIV 58
RRM_Nab3p cd12342
RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) ...
37-110 8.02e-03

RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins; This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues.


Pssm-ID: 240788 [Multi-domain]  Cd Length: 71  Bit Score: 37.42  E-value: 8.02e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156703   37 LFIGNLE-KTTTYHDLRNIFQRFGEIVDIDIKKVngvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGKS 110
Cdd:cd12342      2 LFIGNLPtKRVSKEDLFRIFSPYGHLMQIVIKNA-----FGFVQFDSPQSCRNAIECEQGEMNRGKKLHLEVSKS 71
RRM1_MEI2_EAR1_like cd12275
RNA recognition motif 1 (RRM1) found in Mei2-like proteins and terminal EAR1-like proteins; ...
34-103 8.41e-03

RNA recognition motif 1 (RRM1) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 240721 [Multi-domain]  Cd Length: 71  Bit Score: 37.54  E-value: 8.41e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907156703   34 TRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQYAFLqycDIASVCKAIKKMDGEYLGNNRL 103
Cdd:cd12275      1 SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQTeRISEGIVTVHFY---DIRDAKRAVRELCGRHMQQQAL 68
RRM_SRSF10_SRSF12 cd12312
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and ...
36-107 8.77e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 240758 [Multi-domain]  Cd Length: 84  Bit Score: 37.74  E-value: 8.77e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907156703   36 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI------KKVNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF 107
Cdd:cd12312      2 SLFVRNVADDTRPDDLRREFGRYGPIVDVYIpldfytRRPRG---FAYIQFEDVRDAEDALYYLDRTRFLGREIEIQF 76
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
1508-1775 9.74e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 41.79  E-value: 9.74e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1508 RSPAKEPVEQPRVTRKRlerelQEAVVPPTTPRRGRPPKTRRRAEedgeherkePAETPRPAEGWRSPRSQKSAAAAGPQ 1587
Cdd:PRK12323   375 ATAAAAPVAQPAPAAAA-----PAAAAPAPAAPPAAPAAAPAAAA---------AARAVAAAPARRSPAPEALAAARQAS 440
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1588 GKRGRNEQKVEAAAEAGAQASTREGNPKSRGEREAASEPKRDRRDPSTDKNGPDTFPveVLERKPPEKtykskrgrARST 1667
Cdd:PRK12323   441 ARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPP--PWEELPPEF--------ASPA 510
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156703 1668 RSAMDRAAHQRSLEMAARAAGQAADKEAGPAAASPQESESPQKGSGSSPQLANNPADPDREAEEESASAS------TAPP 1741
Cdd:PRK12323   511 PAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVVAPRPPRASASGLPDMFDGDwpalaaRLPV 590
                          250       260       270
                   ....*....|....*....|....*....|....*.
gi 1907156703 1742 EG--TQLARQIELEQAVQNIAKLPEPSAAAASKGTA 1775
Cdd:PRK12323   591 RGlaQQLARQSELAGVEGDTVRLRVPVPALAEAEVV 626
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH