NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|688563808|ref|XP_009301373|]
View 

zinc finger protein 638 isoform X1 [Danio rerio]

Protein Classification

S phase cyclin A-associated protein in the endoplasmic reticulum; C2H2-type zinc finger protein( domain architecture ID 13116398)

S phase cyclin A-associated protein in the endoplasmic reticulum acts as a CCNA2/CDK2 regulatory protein that transiently maintains CCNA2 in the cytoplasm| Cys2His2 (C2H2)-type zinc finger protein may be involved in transcriptional regulation

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 831-906 8.99e-11

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).


The actual alignment was detected with superfamily member cd12716:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 76  Bit Score: 59.71  E-value: 8.99e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 688563808  831 IVEITNLPEAGVTEEELTNLAKPYGFTETPVIAITQQRAYLQMPNTEAAEKMVKTFSETPAKVKEKeiTVKMMMQP 906
Cdd:cd12716     2 VVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGK--RLKISMAE 75
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 662-731 4.31e-08

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).


The actual alignment was detected with superfamily member cd12436:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 76  Bit Score: 51.96  E-value: 4.31e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 688563808  662 LLRLLGLPIGTTSK-DLTDAIEPFGKIYTAILLKAIREASVCMEREEDARALLN---CKNLTIHGQVIKVCMEK 731
Cdd:cd12436     2 VLYLTGLPVSKYSEeDVLKLAEPFGKVNNVLLIRSKREAFIEMETAEDAQAMLSyckTKPITIKGKKVKVSVSQ 75
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 2135-2169 7.33e-05

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


:

Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 41.85  E-value: 7.33e-05
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 688563808   2135 TGFFCKLCSLFYVNEDtAKKSHCSSLKHYQNMEKY 2169
Cdd:smart00451    2 GGFYCKLCNVTFTDEI-SVEAHLKGKKHKKNVKKR 35
PTZ00121 super family cl31754
MAEBL; Provisional
 1185-2123 1.19e-03

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 44.36  E-value: 1.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1185 VSVESGNADCHVESAVPASESAISVESVNGEHKEGSPASAIESGKADlevksasesavlvESAKAEHELVSPESAIPVET 1264
Cdd:PTZ00121 1066 VGQDEGLKPSYKDFDFDAKEDNRADEATEEAFGKAEEAKKTETGKAE-------------EARKAEEAKKKAEDARKAEE 1132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1265 TEQSEaDSKKDQDVPQAEDAPKEPLSTSVEG--KIEDEKLAEDremelgtsgVSSEEMAVEPMETQSTEETAKDTDVKED 1342
Cdd:PTZ00121 1133 ARKAE-DARKAEEARKAEDAKRVEIARKAEDarKAEEARKAED---------AKKAEAARKAEEVRKAEELRKAEDARKA 1202

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1343 DCK---PQEHIIDSEGQSKELTPTENVgADINPTTKAGANADASDSIPTSDPTSDLPSTSNQAFSNSTVPVTcASESPHV 1419
Cdd:PTZ00121 1203 EAArkaEEERKAEEARKAEDAKKAEAV-KKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIK-AEEARKA 1280

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1420 VPEPFLVNDQSLDFPPVTQEILKALELA--VHQCRLQSSLKRAEEEAKQKAETekkaaekkttkgqsgSKKPAQSTKKAt 1497
Cdd:PTZ00121 1281 DELKKAEEKKKADEAKKAEEKKKADEAKkkAEEAKKADEAKKKAEEAKKKADA---------------AKKKAEEAKKA- 1344

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1498 pAQAKKMQAEKEKKSQSSGSKGKTTDTSSPEKESSSRYRTRGNSDEEGTTRRRGGSSGGSSLRSRRESSPPSKRTRGhdv 1577
Cdd:PTZ00121 1345 -AEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKA--- 1420

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1578 DSRRPSRTHSRTRASVKEKEDEsfSFNFDEFVTVDEVGDDAEDIVASTAESSAMDEnikdepdphtltAQSEADKPKPTD 1657
Cdd:PTZ00121 1421 DEAKKKAEEKKKADEAKKKAEE--AKKADEAKKKAEEAKKAEEAKKKAEEAKKADE------------AKKKAEEAKKAD 1486

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1658 SVvpsETSNSEINACVEELEAKAEETTQVD-VDIAEEQESPEDSSdkpletdiqcKTEKPCTVTETSSAETNTNDESLSA 1736
Cdd:PTZ00121 1487 EA---KKKAEEAKKKADEAKKAAEAKKKADeAKKAEEAKKADEAK----------KAEEAKKADEAKKAEEKKKADELKK 1553

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1737 IKETSGIETLDELEpsHAVSSTQKEGSPPRSAETPEKLEDDHSEQPENSAPEMENKK-EAADQTPELPCHDSLVTLDEVS 1815
Cdd:PTZ00121 1554 AEELKKAEEKKKAE--EAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKaEEAKKAEEAKIKAEELKKAEEE 1631

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1816 EGEEDFIYETNEEQLLKADELPETlltvDEVGDDETGIEEYQLEKDLQGLVTLDEVVDEEEFDPETLVTLDEAKGDDEEL 1895
Cdd:PTZ00121 1632 KKKVEQLKKKEAEEKKKAEELKKA----EEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEEL 1707

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1896 EQSESmpTSPRTTTPIIPEEPVKSPR-------QEDDASYLEELRKMNFVTVDEVGEEEEEEQPPCEEVKEEKPVKKRAT 1968
Cdd:PTZ00121 1708 KKKEA--EEKKKAEELKKAEEENKIKaeeakkeAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEEL 1785

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1969 RGRKRARQTPVRRSTRGKRGSAKVVEEPEEeeepeataepepvpEATIVesppaavesvaLDVQPEQQKAEDMMVTDSLT 2048
Cdd:PTZ00121 1786 DEEDEKRRMEVDKKIKDIFDNFANIIEGGK--------------EGNLV-----------INDSKEMEDSAIKEVADSKN 1840

                         890       900       910       920       930       940       950
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 688563808 2049 AEVSEEDMIKSKDDVGSTKSETDTPDTADSNKKPTIKEESKErrEIDPVEEPEAKRSRSQSPLIEDFTMPPFNPD 2123
Cdd:PTZ00121 1841 MQLEEADAFEKHKFNKNNENGEDGNKEADFNKEKDLKEDDEE--EIEEADEIEKIDKDDIEREIPNNNMAGKNND 1913
 
Name Accession Description Interval E-value
RRM1_2_NP220 cd12716
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); ...
 831-906 8.99e-11

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); This subgroup corresponds to RRM1 and RRM2 of NP220, also termed zinc finger protein 638 (ZN638), or cutaneous T-cell lymphoma-associated antigen se33-1, or zinc finger matrin-like protein, a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). NP220 contains multiple domains, including MH1, MH2, and MH3, domains homologous to the acidic nuclear protein matrin 3; RS, an arginine/serine-rich domain commonly found in pre-mRNA splicing factors; PstI-HindIII, a domain essential for DNA binding; acidic repeat, a domain with nine repeats of the sequence LVTVDEVIEEEDL; and a Cys2-His2 zinc finger-like motif that is also present in matrin 3. It may be involved in packaging, transferring, or processing transcripts. This subgroup corresponds to the domain of MH2 that contains two tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410115 [Multi-domain]  Cd Length: 76  Bit Score: 59.71  E-value: 8.99e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 688563808  831 IVEITNLPEAGVTEEELTNLAKPYGFTETPVIAITQQRAYLQMPNTEAAEKMVKTFSETPAKVKEKeiTVKMMMQP 906
Cdd:cd12716     2 VVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGK--RLKISMAE 75
RRM1_2_MATR3_like cd12436
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; ...
 662-731 4.31e-08

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; This subfamily corresponds to the RRM of the matrin 3 family of nuclear proteins consisting of Matrin 3 (MATR3), nuclear protein 220 (NP220) and similar proteins. MATR3 is a highly conserved inner nuclear matrix protein that has been implicated in various biological processes. NP220 is a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). Both, Matrin 3 and NP220, contain two RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Cys2-His2 zinc finger-like motif at the C-terminal region.


Pssm-ID: 409870 [Multi-domain]  Cd Length: 76  Bit Score: 51.96  E-value: 4.31e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 688563808  662 LLRLLGLPIGTTSK-DLTDAIEPFGKIYTAILLKAIREASVCMEREEDARALLN---CKNLTIHGQVIKVCMEK 731
Cdd:cd12436     2 VLYLTGLPVSKYSEeDVLKLAEPFGKVNNVLLIRSKREAFIEMETAEDAQAMLSyckTKPITIKGKKVKVSVSQ 75
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 2135-2169 7.33e-05

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 41.85  E-value: 7.33e-05
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 688563808   2135 TGFFCKLCSLFYVNEDtAKKSHCSSLKHYQNMEKY 2169
Cdd:smart00451    2 GGFYCKLCNVTFTDEI-SVEAHLKGKKHKKNVKKR 35
PTZ00121 PTZ00121
MAEBL; Provisional
 1185-2123 1.19e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 44.36  E-value: 1.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1185 VSVESGNADCHVESAVPASESAISVESVNGEHKEGSPASAIESGKADlevksasesavlvESAKAEHELVSPESAIPVET 1264
Cdd:PTZ00121 1066 VGQDEGLKPSYKDFDFDAKEDNRADEATEEAFGKAEEAKKTETGKAE-------------EARKAEEAKKKAEDARKAEE 1132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1265 TEQSEaDSKKDQDVPQAEDAPKEPLSTSVEG--KIEDEKLAEDremelgtsgVSSEEMAVEPMETQSTEETAKDTDVKED 1342
Cdd:PTZ00121 1133 ARKAE-DARKAEEARKAEDAKRVEIARKAEDarKAEEARKAED---------AKKAEAARKAEEVRKAEELRKAEDARKA 1202

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1343 DCK---PQEHIIDSEGQSKELTPTENVgADINPTTKAGANADASDSIPTSDPTSDLPSTSNQAFSNSTVPVTcASESPHV 1419
Cdd:PTZ00121 1203 EAArkaEEERKAEEARKAEDAKKAEAV-KKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIK-AEEARKA 1280

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1420 VPEPFLVNDQSLDFPPVTQEILKALELA--VHQCRLQSSLKRAEEEAKQKAETekkaaekkttkgqsgSKKPAQSTKKAt 1497
Cdd:PTZ00121 1281 DELKKAEEKKKADEAKKAEEKKKADEAKkkAEEAKKADEAKKKAEEAKKKADA---------------AKKKAEEAKKA- 1344

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1498 pAQAKKMQAEKEKKSQSSGSKGKTTDTSSPEKESSSRYRTRGNSDEEGTTRRRGGSSGGSSLRSRRESSPPSKRTRGhdv 1577
Cdd:PTZ00121 1345 -AEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKA--- 1420

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1578 DSRRPSRTHSRTRASVKEKEDEsfSFNFDEFVTVDEVGDDAEDIVASTAESSAMDEnikdepdphtltAQSEADKPKPTD 1657
Cdd:PTZ00121 1421 DEAKKKAEEKKKADEAKKKAEE--AKKADEAKKKAEEAKKAEEAKKKAEEAKKADE------------AKKKAEEAKKAD 1486

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1658 SVvpsETSNSEINACVEELEAKAEETTQVD-VDIAEEQESPEDSSdkpletdiqcKTEKPCTVTETSSAETNTNDESLSA 1736
Cdd:PTZ00121 1487 EA---KKKAEEAKKKADEAKKAAEAKKKADeAKKAEEAKKADEAK----------KAEEAKKADEAKKAEEKKKADELKK 1553

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1737 IKETSGIETLDELEpsHAVSSTQKEGSPPRSAETPEKLEDDHSEQPENSAPEMENKK-EAADQTPELPCHDSLVTLDEVS 1815
Cdd:PTZ00121 1554 AEELKKAEEKKKAE--EAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKaEEAKKAEEAKIKAEELKKAEEE 1631

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1816 EGEEDFIYETNEEQLLKADELPETlltvDEVGDDETGIEEYQLEKDLQGLVTLDEVVDEEEFDPETLVTLDEAKGDDEEL 1895
Cdd:PTZ00121 1632 KKKVEQLKKKEAEEKKKAEELKKA----EEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEEL 1707

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1896 EQSESmpTSPRTTTPIIPEEPVKSPR-------QEDDASYLEELRKMNFVTVDEVGEEEEEEQPPCEEVKEEKPVKKRAT 1968
Cdd:PTZ00121 1708 KKKEA--EEKKKAEELKKAEEENKIKaeeakkeAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEEL 1785

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1969 RGRKRARQTPVRRSTRGKRGSAKVVEEPEEeeepeataepepvpEATIVesppaavesvaLDVQPEQQKAEDMMVTDSLT 2048
Cdd:PTZ00121 1786 DEEDEKRRMEVDKKIKDIFDNFANIIEGGK--------------EGNLV-----------INDSKEMEDSAIKEVADSKN 1840

                         890       900       910       920       930       940       950
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 688563808 2049 AEVSEEDMIKSKDDVGSTKSETDTPDTADSNKKPTIKEESKErrEIDPVEEPEAKRSRSQSPLIEDFTMPPFNPD 2123
Cdd:PTZ00121 1841 MQLEEADAFEKHKFNKNNENGEDGNKEADFNKEKDLKEDDEE--EIEEADEIEKIDKDDIEREIPNNNMAGKNND 1913
RRM smart00360
RNA recognition motif;
667-727 1.74e-03

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 39.11  E-value: 1.74e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 688563808    667 GLPIGTTSKDLTDAIEPFGKIYTAILL------KAIREASVCMEREEDA-RALLNCKNLTIHGQVIKV 727
Cdd:smart00360    6 NLPPDTTEEELRELFSKFGKVESVRLVrdketgKSKGFAFVEFESEEDAeKALEALNGKELDGRPLKV 73
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
 667-715 3.64e-03

hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).


Pssm-ID: 273733 [Multi-domain]  Cd Length: 481  Bit Score: 42.11  E-value: 3.64e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 688563808   667 GLPIGTTSKDLTDAIEPFGKIYTAILLKAIREASVCMEREEDARALLNC 715
Cdd:TIGR01649    9 NLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNF 57
 
Name Accession Description Interval E-value
RRM1_2_NP220 cd12716
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); ...
 831-906 8.99e-11

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); This subgroup corresponds to RRM1 and RRM2 of NP220, also termed zinc finger protein 638 (ZN638), or cutaneous T-cell lymphoma-associated antigen se33-1, or zinc finger matrin-like protein, a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). NP220 contains multiple domains, including MH1, MH2, and MH3, domains homologous to the acidic nuclear protein matrin 3; RS, an arginine/serine-rich domain commonly found in pre-mRNA splicing factors; PstI-HindIII, a domain essential for DNA binding; acidic repeat, a domain with nine repeats of the sequence LVTVDEVIEEEDL; and a Cys2-His2 zinc finger-like motif that is also present in matrin 3. It may be involved in packaging, transferring, or processing transcripts. This subgroup corresponds to the domain of MH2 that contains two tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410115 [Multi-domain]  Cd Length: 76  Bit Score: 59.71  E-value: 8.99e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 688563808  831 IVEITNLPEAGVTEEELTNLAKPYGFTETPVIAITQQRAYLQMPNTEAAEKMVKTFSETPAKVKEKeiTVKMMMQP 906
Cdd:cd12716     2 VVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGK--RLKISMAE 75
RRM_RBM20 cd12685
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily ...
 831-902 1.45e-10

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily corresponds to the RRM of RBM20, an alternative splicing regulator associated with dilated cardiomyopathy (DCM). It contains only one copy of RNA-recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410086 [Multi-domain]  Cd Length: 76  Bit Score: 59.18  E-value: 1.45e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 688563808  831 IVEITNLPEAGVTEEELTNLAKPYGFTETPVIAITQQRAYLQMPNTEAAEKMVKTFSETPAKVKEKEITVKM 902
Cdd:cd12685     2 VVHICNLPEGSCTENDVINLGLPFGKVTNYILMRSTNQAFLEMAYTEAAQAMVQYYQEKPAMINEEKLLIRM 73
RRM1_2_MATR3_like cd12436
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; ...
 831-901 1.35e-09

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; This subfamily corresponds to the RRM of the matrin 3 family of nuclear proteins consisting of Matrin 3 (MATR3), nuclear protein 220 (NP220) and similar proteins. MATR3 is a highly conserved inner nuclear matrix protein that has been implicated in various biological processes. NP220 is a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). Both, Matrin 3 and NP220, contain two RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Cys2-His2 zinc finger-like motif at the C-terminal region.


Pssm-ID: 409870 [Multi-domain]  Cd Length: 76  Bit Score: 56.20  E-value: 1.35e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 688563808  831 IVEITNLPEAGVTEEELTNLAKPYGFTETPVIAITQQRAYLQMPNTEAAEKMVKTFSETPAKVKEKEITVK 901
Cdd:cd12436     2 VLYLTGLPVSKYSEEDVLKLAEPFGKVNNVLLIRSKREAFIEMETAEDAQAMLSYCKTKPITIKGKKVKVS 72
RRM1_2_MATR3_like cd12436
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; ...
 662-731 4.31e-08

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; This subfamily corresponds to the RRM of the matrin 3 family of nuclear proteins consisting of Matrin 3 (MATR3), nuclear protein 220 (NP220) and similar proteins. MATR3 is a highly conserved inner nuclear matrix protein that has been implicated in various biological processes. NP220 is a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). Both, Matrin 3 and NP220, contain two RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Cys2-His2 zinc finger-like motif at the C-terminal region.


Pssm-ID: 409870 [Multi-domain]  Cd Length: 76  Bit Score: 51.96  E-value: 4.31e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 688563808  662 LLRLLGLPIGTTSK-DLTDAIEPFGKIYTAILLKAIREASVCMEREEDARALLN---CKNLTIHGQVIKVCMEK 731
Cdd:cd12436     2 VLYLTGLPVSKYSEeDVLKLAEPFGKVNNVLLIRSKREAFIEMETAEDAQAMLSyckTKPITIKGKKVKVSVSQ 75
RRM1_PTBP1_hnRNPL_like cd12421
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
 831-898 2.97e-07

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: 49.50  E-value: 2.97e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 688563808  831 IVEITNLPEaGVTEEELTNLAKPYGFTETPVIAITQQRAYLQMPNTEAAEKMVKTFSETPAKVKEKEI 898
Cdd:cd12421     1 VVHIRNLPP-DATEADLVALGLPFGKVTNVLLLKGKNQALVEMEDVESASSMVNYYTTVPPLIRGRPV 67
RRM2_MATR3 cd12715
RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the ...
 831-900 9.58e-07

RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the RRM2 of Matrin 3 (MATR3 or P130), a highly conserved inner nuclear matrix protein with a bipartite nuclear localization signal (NLS), two zinc finger domains predicted to bind DNA, and two RNA recognition motifs (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that are known to interact with RNA. MATR3 has been implicated in various biological processes. It is involved in RNA processing by interacting with other nuclear proteins to anchor hyperedited RNAs to the nuclear matrix. It plays a role in mRNA stabilization through maintaining the stability of certain mRNA species. Besides, it modulates the activity of proximal promoters by binding to highly repetitive sequences of matrix/scaffold attachment region (MAR/SAR). The phosphorylation of MATR3 is assumed to cause neuronal death. It is phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Its phosphorylation by protein kinase A (PKA) is responsible for the activation of the N-methyl-d-aspartic acid (NMDA) receptor. Furthermore, MATR3 has been identified as both a Ca2+-dependent CaM-binding protein and a downstream substrate of caspases. Additional research indicates that matrin 3 also binds Rev/Rev responsive element (RRE)-containing viral RNA and functions as a cofactor that mediates the post-transcriptional regulation of HIV-1.


Pssm-ID: 410114 [Multi-domain]  Cd Length: 80  Bit Score: 48.29  E-value: 9.58e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808  831 IVEITNLPEAGVTEEELTNLAKPYGFTETPVIAITQQRAYLQMPNTEAAEKMVKTFSETPAKVKEKEITV 900
Cdd:cd12715     2 VIHLSNLPHSGYSDAAVLKLAEPYGKVKNYILMRMKNQAFLEMESREDAMAMVDHCKKKPLWFQGRCVKV 71
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 663-727 2.09e-05

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: 44.20  E-value: 2.09e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 688563808  663 LRLLGLPIGTTSKDLTDAIEPFGKIYTAILLKAIREAS-----VCMEREEDA-RALLNCKNLTIHGQVIKV 727
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSkgfafVEFESPEDAeKALEALNGTELGGRPLKV 71
RRM1_PTBP1_hnRNPL_like cd12421
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
 667-725 2.17e-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 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: 44.49  E-value: 2.17e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 688563808  667 GLPIGTTSKDLTDAIEPFGKIYTAILLKAIREASVCMEREEDARALLNC---KNLTIHGQVI 725
Cdd:cd12421     6 NLPPDATEADLVALGLPFGKVTNVLLLKGKNQALVEMEDVESASSMVNYyttVPPLIRGRPV 67
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 2135-2169 7.33e-05

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 41.85  E-value: 7.33e-05
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 688563808   2135 TGFFCKLCSLFYVNEDtAKKSHCSSLKHYQNMEKY 2169
Cdd:smart00451    2 GGFYCKLCNVTFTDEI-SVEAHLKGKKHKKNVKKR 35
RRM_SCAF4_SCAF8 cd12227
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), ...
 671-727 2.66e-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: 41.27  E-value: 2.66e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 688563808  671 GTTSKDLTDAIEPFGKIYTAILLKAIREASVCMEREEDA-RALLNCKNLTIHGQVIKV 727
Cdd:cd12227    13 KVTQEELKNLFEEYGEIQSIDMIPPRGCAYVCMKTRQDAhRALQKLKNHKLRGKSIKI 70
PTZ00121 PTZ00121
MAEBL; Provisional
 1185-2123 1.19e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 44.36  E-value: 1.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1185 VSVESGNADCHVESAVPASESAISVESVNGEHKEGSPASAIESGKADlevksasesavlvESAKAEHELVSPESAIPVET 1264
Cdd:PTZ00121 1066 VGQDEGLKPSYKDFDFDAKEDNRADEATEEAFGKAEEAKKTETGKAE-------------EARKAEEAKKKAEDARKAEE 1132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1265 TEQSEaDSKKDQDVPQAEDAPKEPLSTSVEG--KIEDEKLAEDremelgtsgVSSEEMAVEPMETQSTEETAKDTDVKED 1342
Cdd:PTZ00121 1133 ARKAE-DARKAEEARKAEDAKRVEIARKAEDarKAEEARKAED---------AKKAEAARKAEEVRKAEELRKAEDARKA 1202

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1343 DCK---PQEHIIDSEGQSKELTPTENVgADINPTTKAGANADASDSIPTSDPTSDLPSTSNQAFSNSTVPVTcASESPHV 1419
Cdd:PTZ00121 1203 EAArkaEEERKAEEARKAEDAKKAEAV-KKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIK-AEEARKA 1280

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1420 VPEPFLVNDQSLDFPPVTQEILKALELA--VHQCRLQSSLKRAEEEAKQKAETekkaaekkttkgqsgSKKPAQSTKKAt 1497
Cdd:PTZ00121 1281 DELKKAEEKKKADEAKKAEEKKKADEAKkkAEEAKKADEAKKKAEEAKKKADA---------------AKKKAEEAKKA- 1344

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1498 pAQAKKMQAEKEKKSQSSGSKGKTTDTSSPEKESSSRYRTRGNSDEEGTTRRRGGSSGGSSLRSRRESSPPSKRTRGhdv 1577
Cdd:PTZ00121 1345 -AEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKA--- 1420

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1578 DSRRPSRTHSRTRASVKEKEDEsfSFNFDEFVTVDEVGDDAEDIVASTAESSAMDEnikdepdphtltAQSEADKPKPTD 1657
Cdd:PTZ00121 1421 DEAKKKAEEKKKADEAKKKAEE--AKKADEAKKKAEEAKKAEEAKKKAEEAKKADE------------AKKKAEEAKKAD 1486

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1658 SVvpsETSNSEINACVEELEAKAEETTQVD-VDIAEEQESPEDSSdkpletdiqcKTEKPCTVTETSSAETNTNDESLSA 1736
Cdd:PTZ00121 1487 EA---KKKAEEAKKKADEAKKAAEAKKKADeAKKAEEAKKADEAK----------KAEEAKKADEAKKAEEKKKADELKK 1553

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1737 IKETSGIETLDELEpsHAVSSTQKEGSPPRSAETPEKLEDDHSEQPENSAPEMENKK-EAADQTPELPCHDSLVTLDEVS 1815
Cdd:PTZ00121 1554 AEELKKAEEKKKAE--EAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKaEEAKKAEEAKIKAEELKKAEEE 1631

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1816 EGEEDFIYETNEEQLLKADELPETlltvDEVGDDETGIEEYQLEKDLQGLVTLDEVVDEEEFDPETLVTLDEAKGDDEEL 1895
Cdd:PTZ00121 1632 KKKVEQLKKKEAEEKKKAEELKKA----EEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEEL 1707

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1896 EQSESmpTSPRTTTPIIPEEPVKSPR-------QEDDASYLEELRKMNFVTVDEVGEEEEEEQPPCEEVKEEKPVKKRAT 1968
Cdd:PTZ00121 1708 KKKEA--EEKKKAEELKKAEEENKIKaeeakkeAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEEL 1785

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1969 RGRKRARQTPVRRSTRGKRGSAKVVEEPEEeeepeataepepvpEATIVesppaavesvaLDVQPEQQKAEDMMVTDSLT 2048
Cdd:PTZ00121 1786 DEEDEKRRMEVDKKIKDIFDNFANIIEGGK--------------EGNLV-----------INDSKEMEDSAIKEVADSKN 1840

                         890       900       910       920       930       940       950
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 688563808 2049 AEVSEEDMIKSKDDVGSTKSETDTPDTADSNKKPTIKEESKErrEIDPVEEPEAKRSRSQSPLIEDFTMPPFNPD 2123
Cdd:PTZ00121 1841 MQLEEADAFEKHKFNKNNENGEDGNKEADFNKEKDLKEDDEE--EIEEADEIEKIDKDDIEREIPNNNMAGKNND 1913
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
 668-727 1.27e-03

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: 39.13  E-value: 1.27e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 688563808  668 LPIGTTSKDLTDAIEPFGKIYTAILLKaiREASVCMEREEDA-RALLNCKNLTIHGQVIKV 727
Cdd:cd12343     7 LPDAATSEELRALFEKYGKVTECDIVK--NYAFVHMEKEEDAeDAIKALNGYEFMGSRINV 65
PTZ00341 PTZ00341
Ring-infected erythrocyte surface antigen; Provisional
 1065-1349 1.51e-03

Ring-infected erythrocyte surface antigen; Provisional


Pssm-ID: 173534 [Multi-domain]  Cd Length: 1136  Bit Score: 44.01  E-value: 1.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1065 EDSIVISDNEVILIESDDEEKLKAKTTAAK-LTEATKDSAVANANTAASENKvelNTQDTKESITvtPDAGSVKKELEAE 1143
Cdd:PTZ00341  857 ENTAKNAAEQILSDEGLDEKKLKKRAESLKkLANAIEKYAGGGKKDKKAKKK---DAKDLSGNIA--HEINLINKELKNQ 931

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1144 SSVTkvePETIKKELEVESSASTSESAAEsvNKELEVTETTVSVESGNADCHVESAVPASESAISVESVNGEHKEGSPAS 1223
Cdd:PTZ00341  932 NENV---PEHLKEHAEANIEEDAEENVEE--DAEENVEENVEENVEENVEENVEENVEENVEENVEENVEENVEENIEEN 1006

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1224 AIESGKADLEVKSASESAVLVESAKAEHELVSPESAIPVETTEQSEADSKKDQDVPQAEDAPKEPLSTSVEGKIEdEKLA 1303
Cdd:PTZ00341 1007 VEENVEENIEENVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEIEENIEENIE-ENVE 1085

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 688563808 1304 EDREMELGTSGVSSEEMAVEPMEtQSTEETAKDTDVKEDDCKPQEH 1349
Cdd:PTZ00341 1086 ENVEENVEEIEENVEENVEENAE-ENAEENAEENAEEYDDENPEEH 1130
RRM smart00360
RNA recognition motif;
667-727 1.74e-03

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 39.11  E-value: 1.74e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 688563808    667 GLPIGTTSKDLTDAIEPFGKIYTAILL------KAIREASVCMEREEDA-RALLNCKNLTIHGQVIKV 727
Cdd:smart00360    6 NLPPDTTEEELRELFSKFGKVESVRLVrdketgKSKGFAFVEFESEEDAeKALEALNGKELDGRPLKV 73
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
 667-715 3.64e-03

hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).


Pssm-ID: 273733 [Multi-domain]  Cd Length: 481  Bit Score: 42.11  E-value: 3.64e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 688563808   667 GLPIGTTSKDLTDAIEPFGKIYTAILLKAIREASVCMEREEDARALLNC 715
Cdd:TIGR01649    9 NLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNF 57
PRK13108 PRK13108
prolipoprotein diacylglyceryl transferase; Reviewed
 1638-1790 4.55e-03

prolipoprotein diacylglyceryl transferase; Reviewed


Pssm-ID: 237284 [Multi-domain]  Cd Length: 460  Bit Score: 41.89  E-value: 4.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1638 EPDPHTLTAQSEADKPKPTDSVVPSETSNSEINACVEELEAK-------AEETTQVDVDIAEEQESPEDSSdkplETDIq 1710
Cdd:PRK13108  297 EREPAELAAAAVASAASAVGPVGPGEPNQPDDVAEAVKAEVAevtdevaAESVVQVADRDGESTPAVEETS----EADI- 371

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1711 cktEKPctVTETSSAETNTNDESLSAikETSGIETLDELEPSHAVSSTQKEgSPPRSAETPEKLEDDH--SEQPENSAPE 1788
Cdd:PRK13108  372 ---ERE--QPGDLAGQAPAAHQVDAE--AASAAPEEPAALASEAHDETEPE-VPEKAAPIPDPAKPDElaVAGPGDDPAE 443


                  ..
gi 688563808 1789 ME 1790
Cdd:PRK13108  444 PD 445
RRM1_hnRNPL_like cd12689
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) ...
 660-714 5.16e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins; This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. 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 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. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410090 [Multi-domain]  Cd Length: 80  Bit Score: 38.02  E-value: 5.16e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 688563808  660 SCLLRLLGLPIGTTSKDLTDAIEPFGKIYTAILLKAIREASVCMEREEDARALLN 714
Cdd:cd12689     2 SPVVHVRGLSEHVTEADLVEALQNFGPISYVTMMPKKRQALVEFEDIEGAKACVN 56
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 832-901 5.72e-03

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: 37.65  E-value: 5.72e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 688563808  832 VEITNLPEaGVTEEELTNLAKPYGftetPVIAITQQR---------AYLQMPNTEAAEKMVKTFSETpaKVKEKEITVK 901
Cdd:cd00590     1 LFVGNLPP-DTTEEDLRELFSKFG----EVVSVRIVRdrdgkskgfAFVEFESPEDAEKALEALNGT--ELGGRPLKVS 72
PTZ00121 PTZ00121
MAEBL; Provisional
 1039-1709 5.92e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 42.05  E-value: 5.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1039 AAAPAESAVKKDEKPSAAAKTVApkEEDSIVISDNEVILIESDDEEKLKAKTTAAKLTEATKDSAVANANTAASENKVEL 1118
Cdd:PTZ00121 1270 AAIKAEEARKADELKKAEEKKKA--DEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEA 1347

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1119 NTQDTKESITVTPDAGSVKKELEAESSVTKVEPETIKKELEVESSASTSESAAESVNKELEvtettvsvESGNADCHVES 1198
Cdd:PTZ00121 1348 AKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKAD--------ELKKAAAAKKK 1419

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1199 AVPASESAISVESVNGEHKEgspasAIESGKADlEVKSASESAVLVESAKAEHElvspESAIPVETTEQSEADSKKDQDV 1278
Cdd:PTZ00121 1420 ADEAKKKAEEKKKADEAKKK-----AEEAKKAD-EAKKKAEEAKKAEEAKKKAE----EAKKADEAKKKAEEAKKADEAK 1489

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1279 PQAEDAPK--EPLSTSVEGKIEDEKLAEDREMELGTSGVSSEEmAVEPMETQSTEETAKDTDVKE-DDCKPQEHIIDSEg 1355
Cdd:PTZ00121 1490 KKAEEAKKkaDEAKKAAEAKKKADEAKKAEEAKKADEAKKAEE-AKKADEAKKAEEKKKADELKKaEELKKAEEKKKAE- 1567

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1356 QSKELTPTENVGADINPTTKAGANADASDSIPTSDPTSDLPSTSNQAFSNSTVPVTCASESPHVVPEPFLVNDQSLDFPP 1435
Cdd:PTZ00121 1568 EAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKK 1647

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1436 VTQEILKALElaVHQCRLQSSLKRAEEEAKQKAETEKKAAEKKTTKGQsgSKKPAQSTKKAtpAQAKKMQAEKEKKSQ-- 1513
Cdd:PTZ00121 1648 KAEELKKAEE--ENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEA--LKKEAEEAKKA--EELKKKEAEEKKKAEel 1721

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1514 --SSGSKGKTTDTSSPEKESSSRYRTRGNSDEEGTTRRRGGSSGGSSLRSRRESSPPSKRTRGHDVDSRRPSRTHSRTRA 1591
Cdd:PTZ00121 1722 kkAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKRRMEVDKKIK 1801

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688563808 1592 SVKEKEDESFSFNFDEFVTVDEVGDDAEDIVASTAESSAMDENIKDEPDPHTLTAQSEADKPKPTDSVVPSETSNSEINa 1671
Cdd:PTZ00121 1802 DIFDNFANIIEGGKEGNLVINDSKEMEDSAIKEVADSKNMQLEEADAFEKHKFNKNNENGEDGNKEADFNKEKDLKEDD- 1880

                         650       660       670
                  ....*....|....*....|....*....|....*...
gi 688563808 1672 cVEELEaKAEETTQVDVDIAEEQESpeDSSDKPLETDI 1709
Cdd:PTZ00121 1881 -EEEIE-EADEIEKIDKDDIEREIP--NNNMAGKNNDI 1914
 
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