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Conserved domains on  [gi|24580581|ref|NP_524718|]
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split ends, isoform B [Drosophila melanogaster]

Protein Classification

Graphical summary

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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 ...
 5372-5533 6.26e-96

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: 307.60  E-value: 6.26e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 5372 RYPVMWQGLLALKTDQAAVQMHFVHGNPNVARASLP-SLVETNTPLLRIAQRMRLEQTQLEGVAKKMQVDKEHCMLLALP 5450
Cdd:cd21543    1 RYPVVWQGLLALKNDEAAVQMHYVSGNQDLAKRSLPrHLTNGNLPPLRIAQRMRLEPSQLEGVARKMQDESEYCLLLALP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 5451 CGRDHADVLQHSRNLQTGFITYLQQKMAAGIVNIPIPGSEQAAYVVHIFPSCDFANENLERAAPDLKNRVAELAHLLIVI 5530
Cdd:cd21543   81 CGRDQEDVLKQTNNLKNGFITYLQQKQAAGIVNVPNPGSQQPAYVVHIFPPCEFSNSHLSRLAPDLLNSIADIPHLMIVI 160


                 ...
gi 24580581 5531 ATV 5533
Cdd:cd21543  161 ATV 163
RRM2_SHARP cd12349
RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 555-628 3.28e-44

RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM2 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: 409785 [Multi-domain]  Cd Length: 74  Bit Score: 156.03  E-value: 3.28e-44
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  555 AIRVRNLPARSSDTSLKDGLFHEYKKHGKVTWVKVVGQNSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEVE 628
Cdd:cd12349    1 GIKVRNLPVRSSDTSLKDGLFHEFKKHGKVTSVKVHGQGEERYAIVFFRRPEDAEKALEVSKGKLFFGMQIEVT 74
RRM3_SHARP cd12350
RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 654-726 2.96e-42

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: 150.64  E-value: 2.96e-42
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  654 STRTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQ-GLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLG 726
Cdd:cd12350    1 ATRTLFIGNLEKTTTYGDLRNIFERFGEIIDIDIKKQnGNPQYAFLQYCDIASVVKAIKKMDGEYLGNNRLKLG 74
RRM4_SHARP cd12351
RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 727-803 2.54e-40

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: 145.21  E-value: 2.54e-40
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581  727 FGKSMPTNCVWIDGVDEKVSESFLQSQFTRFGAVTKVSIDRNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDF 803
Cdd:cd12351    1 FGKSMPTNCVWLDGLSENVTEQYLTRHFCRYGPVVKVVIDRQKGMALVLYDEVECAQAAVKETKGRKIGGRKIQVDF 77
DDRGK super family cl25550
DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and ...
 1998-2072 7.68e-10

DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif.


The actual alignment was detected with superfamily member pfam09756:

Pssm-ID: 370664 [Multi-domain]  Cd Length: 188  Bit Score: 61.59  E-value: 7.68e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581   1998 KEQKeKEIREKDLREKEQRER--DNREKELRDKDLREKEMREKEQREKELHREKdQREREHREKEQSRRAMDVEQEG 2072
Cdd:pfam09756   14 KEAK-RQQREAEEEEREEREKleEKREEEYKEREEREEEAEKEKEEEERKQEEE-QERKEQEEYEKLKSQFVVEEEG 88
Atrophin-1 super family cl38111
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 3577-3804 1.44e-05

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


The actual alignment was detected with superfamily member pfam03154:

Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 51.69  E-value: 1.44e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   3577 PTASQNAMPQASTPKQGPITPQQAIRTQSLIMQPPTISIPEQTPHFAVPQmvlSPQSHHPQQPGTYMVGIRAPSPHSPLH 3656
Cdd:pfam03154  184 PSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQ---TPTLHPQRLPSPHPPLQPMTQPPPPSQ 260

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   3657 SPGRGVAQSRLVGQLSPVGRPMVSQPSPQQQVQQTQQQHALITSPQsSNISPLASPTTRVLSSSNS---PTTSKVNSYQP 3733
Cdd:pfam03154  261 VSPQPLPQPSLHGQMPPMPHSLQTGPSHMQHPVPPQPFPLTPQSSQ-SQVPPGPSPAAPGQSQQRIhtpPSQSQLQSQQP 339

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581   3734 RNQQvPQQPSPKSVAEVQTTPqlmTIPLQKMTPIQVPHHPTIISKVVTVQpqqaTQSQVASSP---PLGSLPPH 3804
Cdd:pfam03154  340 PREQ-PLPPAPLSMPHIKPPP---TTPIPQLPNPQSHKHPPHLSGPSPFQ----MNSNLPPPPalkPLSSLSTH 405
PTZ00121 super family cl31754
MAEBL; Provisional
 1912-2109 3.73e-03

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 43.98  E-value: 3.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  1912 DTADKAEKNQRHEKEKKERQEKREKDLRK--QVEREEKDR----KAQQEEREKEDRKAKEEEKEREREKKAQEDREKKER 1985
Cdd:PTZ00121 1537 DEAKKAEEKKKADELKKAEELKKAEEKKKaeEAKKAEEDKnmalRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAE 1616

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  1986 EERELREKEQRDKEQKEKEIREKDLREKEQRERDNREKELRDKDLREKEMREKEQREKELHREKDQREREHREKEQSRRA 2065
Cdd:PTZ00121 1617 EAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKK 1696

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 24580581  2066 mDVEQEGRGGRMRELSSYQKSKMDIAGEASSLTAIDCQHNKENA 2109
Cdd:PTZ00121 1697 -EAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEA 1739
petO super family cl45540
Cytochrome b6-f complex subunit petO; Chloroplastic cytochrome b6-f complex subunit petO (or ...
 4587-4709 3.78e-03

Cytochrome b6-f complex subunit petO; Chloroplastic cytochrome b6-f complex subunit petO (or PETO), also called cytochrome b6-f complex subunit V (suV) or cytochrome b6-f-associated phosphoprotein, is a novel cytochrome b6-f subunit specific in green algae that is predicted by sequence analysis and biochemical characterization to have a one transmembrane alpha-helix topology with two large hydrophilic domains extending on the stromal and lumenal side of the thylakoid membranes, with a lumenal location of the N-terminus. It is reversibly phosphorylated upon state transition, and may have a possible role in signal transduction during redox-controlled short term and long term adaptation of the eukaryotic photosynthetic apparatus. PetO has been shown to contribute to the cyclic electron flow (CEF) around photosystem I (PSI) and cytochrome b6-f that generates ATP.


The actual alignment was detected with superfamily member cd22950:

Pssm-ID: 438570  Cd Length: 165  Bit Score: 41.39  E-value: 3.78e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 4587 IEEVTASNATVAASHL--APPEGAGVESHVPQLDAkevepvsvVTPISTPAPVSVAAPVTVPVPAMVPVKPTmPQHPKKK 4664
Cdd:cd22950   12 AEEQAQAAAAAAAAALltASPANAGVVLQQPELKK--------VFQDDSPAAAAPKREFKGPPALPAPTAAA-PAAAKEK 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 24580581 4665 AiaAAEIESyqainssiPSGGLPMHQTAAPATQKITGGVADAVSK 4709
Cdd:cd22950   83 K--AEVVES--------SSGGLDPRSVALPAALVFVIGGAFAASK 117
 
Name Accession Description Interval E-value
SPOC_SHARP cd21543
SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor ...
 5372-5533 6.26e-96

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: 307.60  E-value: 6.26e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 5372 RYPVMWQGLLALKTDQAAVQMHFVHGNPNVARASLP-SLVETNTPLLRIAQRMRLEQTQLEGVAKKMQVDKEHCMLLALP 5450
Cdd:cd21543    1 RYPVVWQGLLALKNDEAAVQMHYVSGNQDLAKRSLPrHLTNGNLPPLRIAQRMRLEPSQLEGVARKMQDESEYCLLLALP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 5451 CGRDHADVLQHSRNLQTGFITYLQQKMAAGIVNIPIPGSEQAAYVVHIFPSCDFANENLERAAPDLKNRVAELAHLLIVI 5530
Cdd:cd21543   81 CGRDQEDVLKQTNNLKNGFITYLQQKQAAGIVNVPNPGSQQPAYVVHIFPPCEFSNSHLSRLAPDLLNSIADIPHLMIVI 160


                 ...
gi 24580581 5531 ATV 5533
Cdd:cd21543  161 ATV 163
RRM2_SHARP cd12349
RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 555-628 3.28e-44

RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM2 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: 409785 [Multi-domain]  Cd Length: 74  Bit Score: 156.03  E-value: 3.28e-44
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  555 AIRVRNLPARSSDTSLKDGLFHEYKKHGKVTWVKVVGQNSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEVE 628
Cdd:cd12349    1 GIKVRNLPVRSSDTSLKDGLFHEFKKHGKVTSVKVHGQGEERYAIVFFRRPEDAEKALEVSKGKLFFGMQIEVT 74
RRM3_SHARP cd12350
RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 654-726 2.96e-42

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: 150.64  E-value: 2.96e-42
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  654 STRTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQ-GLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLG 726
Cdd:cd12350    1 ATRTLFIGNLEKTTTYGDLRNIFERFGEIIDIDIKKQnGNPQYAFLQYCDIASVVKAIKKMDGEYLGNNRLKLG 74
RRM4_SHARP cd12351
RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 727-803 2.54e-40

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: 145.21  E-value: 2.54e-40
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581  727 FGKSMPTNCVWIDGVDEKVSESFLQSQFTRFGAVTKVSIDRNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDF 803
Cdd:cd12351    1 FGKSMPTNCVWLDGLSENVTEQYLTRHFCRYGPVVKVVIDRQKGMALVLYDEVECAQAAVKETKGRKIGGRKIQVDF 77
SPOC pfam07744
SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in ...
 5369-5533 6.90e-23

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


Pssm-ID: 400205  Cd Length: 142  Bit Score: 97.81  E-value: 6.90e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   5369 LLQRYPVMWQGLLALKT-DQAAVQMHFVHGNPNVARASLpslvetntplLRIAQRMRLEQTQ--LEGVAKKMqvdkeHCM 5445
Cdd:pfam07744    1 SLQDLEVIWQGTLAMKGvAEFSVRAHLVSGDIDSLLPSL----------LRITGRIRLDAVWkyLDEVRRSI-----TRD 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   5446 LLAL-PCGRDHADVLQhsrnlQTGFITYLQQKMAAGIVNipiPGSEQaAYVVHIFPSCDFAnENLERAAPDLKNRVAEla 5524
Cdd:pfam07744   66 VLVVrFFPSSESDESA-----FDELIDYLQSKQRAGVIH---AKSAD-VKDLYLFPPCEFL-ELLLPVGLSLEVSEPN-- 133


                   ....*....
gi 24580581   5525 HLLIVIATV 5533
Cdd:pfam07744  134 LLLGVVVRK 142
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 556-806 5.90e-16

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: 85.24  E-value: 5.90e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    556 IRVRNLPARSSDTSLKDglfhEYKKHGKVTWVKVV----GQnSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEVEPYQ 631
Cdd:TIGR01628   91 IFVKNLDKSVDNKALFD----TFSKFGNILSCKVAtdenGK-SRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFI 165

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    632 gydvedNEFRPYEAELDEYhpkstRTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQGLN---AYAFCQYSDIVSVVK 708
Cdd:TIGR01628  166 ------KKHEREAAPLKKF-----TNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGrsrGFAFVNFEKHEDAAK 234

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    709 AMRKMDGEHLG----SNRIKLG-----------------------FGKSMPTNcVWIDGVDEKVSESFLQSQFTRFGAVT 761
Cdd:TIGR01628  235 AVEEMNGKKIGlakeGKKLYVGraqkraereaelrrkfeelqqerKMKAQGVN-LYVKNLDDTVTDEKLRELFSECGEIT 313

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|
gi 24580581    762 --KVSID---RNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDFASR 806
Cdd:TIGR01628  314 saKVMLDekgVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQR 363
RRM smart00360
RNA recognition motif;
657-725 5.61e-14

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 69.93  E-value: 5.61e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24580581     657 TLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQGLNA----YAFCQYSDIVSVVKAMRKMDGEHLGSNRIKL 725
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 ...
 658-724 2.05e-11

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: 62.64  E-value: 2.05e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQGLNA---YAFCQYSDIVSVVKAMRKMDGEHLGSNRIK 724
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRskgFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
DDRGK pfam09756
DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and ...
 1998-2072 7.68e-10

DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif.


Pssm-ID: 370664 [Multi-domain]  Cd Length: 188  Bit Score: 61.59  E-value: 7.68e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581   1998 KEQKeKEIREKDLREKEQRER--DNREKELRDKDLREKEMREKEQREKELHREKdQREREHREKEQSRRAMDVEQEG 2072
Cdd:pfam09756   14 KEAK-RQQREAEEEEREEREKleEKREEEYKEREEREEEAEKEKEEEERKQEEE-QERKEQEEYEKLKSQFVVEEEG 88
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 657-801 1.33e-07

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: 58.28  E-value: 1.33e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    657 TLFIGNLEKDITAGELRSHFEAFGEIIEI----DIKKQGLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFG---- 728
Cdd:TIGR01628    2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVrvcrDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSqrdp 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    729 ---KSMPTNcVWIDGVDEKVSESFLQSQFTRFGAVT--KVSIDRN---RQLALVLYDQVQNAQAAVKDMRGTILRRKKLQ 800
Cdd:TIGR01628   82 slrRSGVGN-IFVKNLDKSVDNKALFDTFSKFGNILscKVATDENgksRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVY 160


                   .
gi 24580581    801 V 801
Cdd:TIGR01628  161 V 161
RRM smart00360
RNA recognition motif;
556-627 1.44e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 51.83  E-value: 1.44e-07
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581     556 IRVRNLPARSSDTSLKDgLFheyKKHGKVTWVKVV----GQNSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEV 627
Cdd:smart00360    2 LFVGNLPPDTTEEELRE-LF---SKFGKVESVRLVrdkeTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 3577-3804 1.44e-05

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 51.69  E-value: 1.44e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   3577 PTASQNAMPQASTPKQGPITPQQAIRTQSLIMQPPTISIPEQTPHFAVPQmvlSPQSHHPQQPGTYMVGIRAPSPHSPLH 3656
Cdd:pfam03154  184 PSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQ---TPTLHPQRLPSPHPPLQPMTQPPPPSQ 260

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   3657 SPGRGVAQSRLVGQLSPVGRPMVSQPSPQQQVQQTQQQHALITSPQsSNISPLASPTTRVLSSSNS---PTTSKVNSYQP 3733
Cdd:pfam03154  261 VSPQPLPQPSLHGQMPPMPHSLQTGPSHMQHPVPPQPFPLTPQSSQ-SQVPPGPSPAAPGQSQQRIhtpPSQSQLQSQQP 339

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581   3734 RNQQvPQQPSPKSVAEVQTTPqlmTIPLQKMTPIQVPHHPTIISKVVTVQpqqaTQSQVASSP---PLGSLPPH 3804
Cdd:pfam03154  340 PREQ-PLPPAPLSMPHIKPPP---TTPIPQLPNPQSHKHPPHLSGPSPFQ----MNSNLPPPPalkPLSSLSTH 405
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
655-724 1.51e-05

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 46.24  E-value: 1.51e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581  655 TRTLFIGNLEKDITAGELRSHFEAFGEIIEIDI-------KKQGlnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRIK 724
Cdd:COG0724    1 SMKIYVGNLPYSVTEEDLRELFSEYGEVTSVKLitdretgRSRG---FGFVEMPDDEEAQAAIEALNGAELMGRTLK 74
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
 655-793 1.24e-04

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: 48.01  E-value: 1.24e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    655 TRTLFIGN-LEKDITAGELRSHFEAFGEI-----IEIDIKKQGLnAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFG 728
Cdd:TIGR01661    2 SKTNLIVNyLPQTMTQEEIRSLFTSIGEIescklVRDKVTGQSL-GYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24580581    729 K----SMPTNCVWIDGVDEKVSESFLQSQFTRFGAVTKVSI------DRNRQLALVLYDQVQNAQAAVKDMRGTI 793
Cdd:TIGR01661   81 RpssdSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRIlsdnvtGLSKGVGFIRFDKRDEADRAIKTLNGTT 155
PRK12704 PRK12704
phosphodiesterase; Provisional
 1999-2099 2.32e-03

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 44.38  E-value: 2.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  1999 EQKEKEIREKDLREKEQRERDN----REKELRDKDLR-EKEMREKEQREKELhrEKDQREREHREKEQSRRAMDVEqegr 2073
Cdd:PRK12704   61 EAKEEIHKLRNEFEKELRERRNelqkLEKRLLQKEENlDRKLELLEKREEEL--EKKEKELEQKQQELEKKEEELE---- 134

                          90       100
                  ....*....|....*....|....*.
gi 24580581  2074 ggrmrELSSYQKSKMDiagEASSLTA 2099
Cdd:PRK12704  135 -----ELIEEQLQELE---RISGLTA 152
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 1938-2071 2.85e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 44.16  E-value: 2.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 1938 LRKQVEREEKDRKAQQEERekedrkakeeekererekkaqedrekkereerELREKEQRDKEQKEKEIREKDLREKEQRE 2017
Cdd:COG1196  293 LLAELARLEQDIARLEERR--------------------------------RELEERLEELEEELAELEEELEELEEELE 340

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 24580581 2018 RDNREKELRDKDLREKEMREKEQREKELHREKDQREREHREKEQSRRAMDVEQE 2071
Cdd:COG1196  341 ELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRA 394
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 1997-2073 3.48e-03

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: 43.75  E-value: 3.48e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1997 DKEQKEKEIREKDL-REKE-QRERDNREKELRDKD-LREKEMREKEQREKELHREkdqREREHREKEQSRRAMDVEQEGR 2073
Cdd:TIGR01622   18 DRDRRRDKGRERSRdRSRDrERSRSRRRDRHRDRDyYRGRERRSRSRRPNRRYRP---REKRRRRGDSYRRRRDDRRSRR 94
PTZ00121 PTZ00121
MAEBL; Provisional
 1912-2109 3.73e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 43.98  E-value: 3.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  1912 DTADKAEKNQRHEKEKKERQEKREKDLRK--QVEREEKDR----KAQQEEREKEDRKAKEEEKEREREKKAQEDREKKER 1985
Cdd:PTZ00121 1537 DEAKKAEEKKKADELKKAEELKKAEEKKKaeEAKKAEEDKnmalRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAE 1616

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  1986 EERELREKEQRDKEQKEKEIREKDLREKEQRERDNREKELRDKDLREKEMREKEQREKELHREKDQREREHREKEQSRRA 2065
Cdd:PTZ00121 1617 EAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKK 1696

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 24580581  2066 mDVEQEGRGGRMRELSSYQKSKMDIAGEASSLTAIDCQHNKENA 2109
Cdd:PTZ00121 1697 -EAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEA 1739
petO cd22950
Cytochrome b6-f complex subunit petO; Chloroplastic cytochrome b6-f complex subunit petO (or ...
 4587-4709 3.78e-03

Cytochrome b6-f complex subunit petO; Chloroplastic cytochrome b6-f complex subunit petO (or PETO), also called cytochrome b6-f complex subunit V (suV) or cytochrome b6-f-associated phosphoprotein, is a novel cytochrome b6-f subunit specific in green algae that is predicted by sequence analysis and biochemical characterization to have a one transmembrane alpha-helix topology with two large hydrophilic domains extending on the stromal and lumenal side of the thylakoid membranes, with a lumenal location of the N-terminus. It is reversibly phosphorylated upon state transition, and may have a possible role in signal transduction during redox-controlled short term and long term adaptation of the eukaryotic photosynthetic apparatus. PetO has been shown to contribute to the cyclic electron flow (CEF) around photosystem I (PSI) and cytochrome b6-f that generates ATP.


Pssm-ID: 438570  Cd Length: 165  Bit Score: 41.39  E-value: 3.78e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 4587 IEEVTASNATVAASHL--APPEGAGVESHVPQLDAkevepvsvVTPISTPAPVSVAAPVTVPVPAMVPVKPTmPQHPKKK 4664
Cdd:cd22950   12 AEEQAQAAAAAAAAALltASPANAGVVLQQPELKK--------VFQDDSPAAAAPKREFKGPPALPAPTAAA-PAAAKEK 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 24580581 4665 AiaAAEIESyqainssiPSGGLPMHQTAAPATQKITGGVADAVSK 4709
Cdd:cd22950   83 K--AEVVES--------SSGGLDPRSVALPAALVFVIGGAFAASK 117
 
Name Accession Description Interval E-value
SPOC_SHARP cd21543
SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor ...
 5372-5533 6.26e-96

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: 307.60  E-value: 6.26e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 5372 RYPVMWQGLLALKTDQAAVQMHFVHGNPNVARASLP-SLVETNTPLLRIAQRMRLEQTQLEGVAKKMQVDKEHCMLLALP 5450
Cdd:cd21543    1 RYPVVWQGLLALKNDEAAVQMHYVSGNQDLAKRSLPrHLTNGNLPPLRIAQRMRLEPSQLEGVARKMQDESEYCLLLALP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 5451 CGRDHADVLQHSRNLQTGFITYLQQKMAAGIVNIPIPGSEQAAYVVHIFPSCDFANENLERAAPDLKNRVAELAHLLIVI 5530
Cdd:cd21543   81 CGRDQEDVLKQTNNLKNGFITYLQQKQAAGIVNVPNPGSQQPAYVVHIFPPCEFSNSHLSRLAPDLLNSIADIPHLMIVI 160


                 ...
gi 24580581 5531 ATV 5533
Cdd:cd21543  161 ATV 163
RRM2_SHARP cd12349
RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 555-628 3.28e-44

RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM2 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: 409785 [Multi-domain]  Cd Length: 74  Bit Score: 156.03  E-value: 3.28e-44
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  555 AIRVRNLPARSSDTSLKDGLFHEYKKHGKVTWVKVVGQNSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEVE 628
Cdd:cd12349    1 GIKVRNLPVRSSDTSLKDGLFHEFKKHGKVTSVKVHGQGEERYAIVFFRRPEDAEKALEVSKGKLFFGMQIEVT 74
RRM3_SHARP cd12350
RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 654-726 2.96e-42

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: 150.64  E-value: 2.96e-42
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  654 STRTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQ-GLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLG 726
Cdd:cd12350    1 ATRTLFIGNLEKTTTYGDLRNIFERFGEIIDIDIKKQnGNPQYAFLQYCDIASVVKAIKKMDGEYLGNNRLKLG 74
RRM4_SHARP cd12351
RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 727-803 2.54e-40

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: 145.21  E-value: 2.54e-40
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581  727 FGKSMPTNCVWIDGVDEKVSESFLQSQFTRFGAVTKVSIDRNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDF 803
Cdd:cd12351    1 FGKSMPTNCVWLDGLSENVTEQYLTRHFCRYGPVVKVVIDRQKGMALVLYDEVECAQAAVKETKGRKIGGRKIQVDF 77
SPOC_Spen cd21539
SPOC (Spen paralog and ortholog C-terminal) domain found in the Spen (split end) protein ...
 5376-5531 4.38e-30

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: 118.76  E-value: 4.38e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 5376 MWQGLLALKTDQAAVQMHFVHGNPNVAraSLPSLVETNT-PLLRIAQRMRLEQTQLEGVakKMQVDKEHCMLLALPCGRD 5454
Cdd:cd21539    1 IWRGVLLVKNSAFLFRCHLAKGDAEIA--SQQLLRETVScPQVDIVQRMRLDELALFER--SGAVATGLAILLALPCGDD 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581 5455 HADVLQHSRNLQTGFITYLQQKMAAGIVNIPIPgseQAAYVVHIFPSCDFANENLERAAPDLKNRVAElaHLLIVIA 5531
Cdd:cd21539   77 SISSASITEAPLTNFVSYLKAKQAAGVVLLSDD---HENYVLLLFPPSEFSLSLLKRSLNSEQATSDS--YLVMVVV 148
SPOC_RBM15-like cd21544
SPOC (Spen paralog and ortholog C-terminal) domain found in RNA binding motif protein 15 ...
 5377-5530 1.02e-29

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: 118.15  E-value: 1.02e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 5377 WQGLLALKTDQAAVQMHFVHGNPNVARASLPSLVETNTPLLRIAQRMRLEQTQLEGVAKKMQV--DKEHCMLLALP---C 5451
Cdd:cd21544    2 WSGALVLKNSAFPVRMHLLRGDVQLADTLLPNPTSGEQPVLRITQRLRLDPPKLDDVSRRISSagSSGYCVLLAVPgsgA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 5452 GRDHADVLQHS--RNLqtgfITYLQQKMAAGIVNIP---IPGSEQAAYVVHIFPSCDFANENLERAAPDLKNRVAELAHL 5526
Cdd:cd21544   82 NSEADASTQQRplRNL----VSYLKQKEAAGVVSLPpngSVGEKKVTGVLHAFPPCDFSQQLLRRLAPSLSLESLKDDHL 157


                 ....
gi 24580581 5527 LIVI 5530
Cdd:cd21544  158 VIVL 161
SPOC_SF cd21520
SPOC (Spen paralog and ortholog C-terminal) domain superfamily; The SPOC domain is involved in ...
 5377-5531 5.65e-25

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: 103.52  E-value: 5.65e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 5377 WQGLLALKTDQ-AAVQMHFVHGNPNVARASLPslvetntPLLRIAQRMRLEQTQLEGVAKKMQVDKEHCMLLALPCGRDh 5455
Cdd:cd21520    2 WQGLLALKNDPtAAARLHFVSGNNVLALSELP-------PVLRIAQRMRLNATQLEGVARRMAVATDYCLVLALPCGRD- 73

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581 5456 advlqhSRNLQTGFITYLQQKMAAGIVnipipgSEQAAYVVHIFPSCDFANENLERAAPDL-KNRVAELAHLLIVIA 5531
Cdd:cd21520   74 ------DESLKAAFITYLQAKQRAGIA------SNQPAYVLQLFPPCEFSESHLSRLAPDLlASIVTISPHLMIVIL 138
SPOC pfam07744
SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in ...
 5369-5533 6.90e-23

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


Pssm-ID: 400205  Cd Length: 142  Bit Score: 97.81  E-value: 6.90e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   5369 LLQRYPVMWQGLLALKT-DQAAVQMHFVHGNPNVARASLpslvetntplLRIAQRMRLEQTQ--LEGVAKKMqvdkeHCM 5445
Cdd:pfam07744    1 SLQDLEVIWQGTLAMKGvAEFSVRAHLVSGDIDSLLPSL----------LRITGRIRLDAVWkyLDEVRRSI-----TRD 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   5446 LLAL-PCGRDHADVLQhsrnlQTGFITYLQQKMAAGIVNipiPGSEQaAYVVHIFPSCDFAnENLERAAPDLKNRVAEla 5524
Cdd:pfam07744   66 VLVVrFFPSSESDESA-----FDELIDYLQSKQRAGVIH---AKSAD-VKDLYLFPPCEFL-ELLLPVGLSLEVSEPN-- 133


                   ....*....
gi 24580581   5525 HLLIVIATV 5533
Cdd:pfam07744  134 LLLGVVVRK 142
RRM2_Spen cd12309
RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily ...
 654-729 4.87e-19

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: 84.37  E-value: 4.87e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  654 STRTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKK----QGlNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFGK 729
Cdd:cd12309    1 ATRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRpprgQG-NAYAFVKFLNLDMAHRAKVAMSGQYIGRNQIKIGYGK 79
SPOC_RBM15 cd21549
SPOC (Spen paralog and ortholog C-terminal) domain found in vertebrate RNA binding motif ...
 5377-5530 8.69e-19

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: 86.87  E-value: 8.69e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 5377 WQGLLALKTDQAAVQMHFVHGNPNVARaSLpsLVETNT----PLLRIAQRMRLEQTQLEGVAKKMQV--DKEHCMLLALP 5450
Cdd:cd21549    2 WQGMLLLKNSNFPSNMHLLEGDLSVAS-SL--LVDGSTggkvAQLKITQRLRLDQPKLDEVTRRIKVagPNGYAVLLAVP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 5451 CGRDHADVLQHSRNLQ---TGFITYLQQKMAAGIVNIPIPGSEQA--AYVVHIFPSCDFANENLERAAPDLKNrvAELAH 5525
Cdd:cd21549   79 GSSEVSSVSDQATSTQrplRNLVSYLKQKQAAGVISLPVGGSKDKdnTGVLHAFPPCDFSQQFLDSSAKALAK--SEEDY 156


                 ....*
gi 24580581 5526 LLIVI 5530
Cdd:cd21549  157 LVMII 161
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 556-806 5.90e-16

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: 85.24  E-value: 5.90e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    556 IRVRNLPARSSDTSLKDglfhEYKKHGKVTWVKVV----GQnSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEVEPYQ 631
Cdd:TIGR01628   91 IFVKNLDKSVDNKALFD----TFSKFGNILSCKVAtdenGK-SRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFI 165

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    632 gydvedNEFRPYEAELDEYhpkstRTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQGLN---AYAFCQYSDIVSVVK 708
Cdd:TIGR01628  166 ------KKHEREAAPLKKF-----TNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGrsrGFAFVNFEKHEDAAK 234

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    709 AMRKMDGEHLG----SNRIKLG-----------------------FGKSMPTNcVWIDGVDEKVSESFLQSQFTRFGAVT 761
Cdd:TIGR01628  235 AVEEMNGKKIGlakeGKKLYVGraqkraereaelrrkfeelqqerKMKAQGVN-LYVKNLDDTVTDEKLRELFSECGEIT 313

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|
gi 24580581    762 --KVSID---RNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDFASR 806
Cdd:TIGR01628  314 saKVMLDekgVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQR 363
RRM smart00360
RNA recognition motif;
657-725 5.61e-14

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 69.93  E-value: 5.61e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24580581     657 TLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQGLNA----YAFCQYSDIVSVVKAMRKMDGEHLGSNRIKL 725
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGkskgFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM2_RBM15 cd12555
RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
 653-732 6.89e-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: 70.27  E-value: 6.89e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  653 KSTRTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQG---LNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFGK 729
Cdd:cd12555    5 RANRTLFLGNLDITVTENDLRRAFDRFGVITEVDIKRPGrgqTSTYGFLKFENLDMAHRAKLAMSGKVIGRNPIKIGYGK 84


                 ...
gi 24580581  730 SMP 732
Cdd:cd12555   85 ATP 87
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 574-792 1.48e-13

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: 77.54  E-value: 1.48e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    574 LFHEYKKHGKVTWVKV----VGQNSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEVEpyqgYDVEDNEFRpyeaelde 649
Cdd:TIGR01628   17 LYDLFKPFGPVLSVRVcrdsVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIM----WSQRDPSLR-------- 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    650 yhpKS-TRTLFIGNLEKDITAGELRSHFEAFGEIIEIDI------KKQGlnaYAFCQYSDIVSVVKAMRKMDGEHLGSNR 722
Cdd:TIGR01628   85 ---RSgVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVatdengKSRG---YGFVHFEKEESAKAAIQKVNGMLLNDKE 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    723 IKLgfGKSMP------------TNcVWIDGVDEKVSESFLQSQFTRFGAVT--KVSIDRNRQ---LALVLYDQVQNAQAA 785
Cdd:TIGR01628  159 VYV--GRFIKkhereaaplkkfTN-LYVKNLDPSVNEDKLRELFAKFGEITsaAVMKDGSGRsrgFAFVNFEKHEDAAKA 235


                   ....*..
gi 24580581    786 VKDMRGT 792
Cdd:TIGR01628  236 VEEMNGK 242
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 658-725 1.62e-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: 68.46  E-value: 1.62e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQGLNA---YAFCQYSDIVSVVKAMRKMDGEHLGSNRIKL 725
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKskgFAFVEFESPEDAEKALEALNGTELGGRPLKV 71
SPOC_RBM15B cd21550
SPOC (Spen paralog and ortholog C-terminal) domain found in putative RNA binding motif protein ...
 5377-5530 2.24e-13

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: 71.43  E-value: 2.24e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 5377 WQGLLALKTDQAAVQMHFVHGNPNVARASLPSLVE-TNTPLLRIAQRMRLEQTQLEGVAKKMQVDKE--HCMLLALPCGR 5453
Cdd:cd21550    2 WNGVLVLKNSCFPTNMHILEGDLGVVNILLKDYTSgGKLTQLKIAQRLRLDQPKLDEVTRRIKQGSPdgYAVLLATQAPQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 5454 DHADV--------LQhsRNLQTGFITYLQQKMAAGIVNIPIPGSEQAAY--VVHIFPSCDFANENLERAAPDLKNRVAEl 5523
Cdd:cd21550   82 GGEGGgappvepgLQ--RRLLRNLVSYLKQKQAAGVISLPVGGSKDRDNtgMLYAFPPCDFSQQYLQSALRTLGKLEEE- 158


                 ....*..
gi 24580581 5524 aHLLIVI 5530
Cdd:cd21550  159 -HMVIVI 164
RRM1_Spen cd12308
RNA recognition motif 1 (RRM1) found in the Spen (split end) protein family; This subfamily ...
 556-631 1.92e-12

RNA recognition motif 1 (RRM1) found in the Spen (split end) protein family; This subfamily corresponds to the RRM1 domain in the Spen (split end) 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 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 known as 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: 409749 [Multi-domain]  Cd Length: 78  Bit Score: 65.73  E-value: 1.92e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24580581  556 IRVRNLPARSSDTSLKDGLFHEYKKHGKVTwVKVVGQNSERYALVCFKKPDDvekALEVSHDK---HFFGCKIEVEPYQ 631
Cdd:cd12308    4 LCVSNLPAKLSDEEIEDVLYHEFKKFGDVS-VRLQHDGDERVAYVNFRHPED---AREAKHAKlrlVLFDRPLNVEPVY 78
RRM2_RBM15B cd12556
RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from ...
 653-729 2.69e-12

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: 65.71  E-value: 2.69e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  653 KSTRTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKK----QGlNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFG 728
Cdd:cd12556    6 RATRNLFIGNLDHNVSEVELRRAFEKYGIIEEVVIKRpargQG-GAYAFLKFQNLDMAHRAKVAMSGRVIGRNPIKIGYG 84


                 .
gi 24580581  729 K 729
Cdd:cd12556   85 K 85
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 658-724 2.05e-11

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: 62.64  E-value: 2.05e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQGLNA---YAFCQYSDIVSVVKAMRKMDGEHLGSNRIK 724
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRskgFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 558-772 7.44e-10

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: 65.33  E-value: 7.44e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    558 VRNLPARSSDTSLKDglFheYKKHGKVTWVKVV-GQNSER---YALVCFKKPDDVEKALEVSHDKhFFGCKIEVEPYQGy 633
Cdd:TIGR01622  119 VQQLAARARERDLYE--F--FSKVGKVRDVQIIkDRNSRRskgVGYVEFYDVDSVQAALALTGQK-LLGIPVIVQLSEA- 192

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    634 dvEDNEFRPYEAELDEYHPKST--RTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQG----LNAYAFCQYSDIVSVV 707
Cdd:TIGR01622  193 --EKNRAARAATETSGHHPNSIpfHRLYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKDPetgrSKGYGFIQFRDAEQAK 270

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581    708 KAMRKMDGEHLGSNRIKLGFG-KSMPTNcvwiDGVDEKVSESFLQSQFTRFGAVTKVSIDRNRQLA 772
Cdd:TIGR01622  271 EALEKMNGFELAGRPIKVGLGnDFTPES----DANLAQRFQDQDGSAFSGAGLNTPARSQLMRKLA 332
DDRGK pfam09756
DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and ...
 1998-2072 7.68e-10

DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif.


Pssm-ID: 370664 [Multi-domain]  Cd Length: 188  Bit Score: 61.59  E-value: 7.68e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581   1998 KEQKeKEIREKDLREKEQRER--DNREKELRDKDLREKEMREKEQREKELHREKdQREREHREKEQSRRAMDVEQEG 2072
Cdd:pfam09756   14 KEAK-RQQREAEEEEREEREKleEKREEEYKEREEREEEAEKEKEEEERKQEEE-QERKEQEEYEKLKSQFVVEEEG 88
RRM3_Spen cd12310
RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily ...
 736-804 1.67e-09

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: 57.29  E-value: 1.67e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24580581  736 VWIDGVDEKVSESFLQSQFTRFGAVTKVSIDRNRQLALVLYDQVQNAQAAVKDMRGTILRR--KKLQVDFA 804
Cdd:cd12310    1 LWVGGLGPWTSLAELEREFDRFGAIRKIDYRKGDDYAYILYESLDAAQAAVRALRGFPLGGpdRRLRVDFA 71
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 556-628 2.66e-09

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: 56.52  E-value: 2.66e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581  556 IRVRNLPARSSDTSLKDgLFheyKKHGKVTWVKVV---GQNSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEVE 628
Cdd:cd00590    1 LFVGNLPPDTTEEDLRE-LF---SKFGEVVSVRIVrdrDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RRM1_RBM15 cd12553
RNA recognition motif 1 (RRM1) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
 555-611 4.09e-09

RNA recognition motif 1 (RRM1) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM1 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 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 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: 409969 [Multi-domain]  Cd Length: 78  Bit Score: 56.11  E-value: 4.09e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581  555 AIRVRNLPARSSDTSLKDGLFHEYKKHGKVTwVKVVGQNSERYALVCFKKPDDVEKA 611
Cdd:cd12553    3 TLKISELGSQLSDEAVEDGLFHEFKKFGDVS-VKISRLGDERVAFVNFRRPEDARAA 58
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
 657-728 4.85e-09

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: 55.79  E-value: 4.85e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24580581  657 TLFIGNLEKDITAGELRSHFEAFGEIIEIDI---KKQGlnayaFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFG 728
Cdd:cd12346    3 TVFVGGLDPNVTEEDLRVLFGPFGEIVYVKIppgKGCG-----FVQFVNRASAEAAIQKLQGTPIGGSRIRLSWG 72
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
 655-729 1.74e-08

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: 54.33  E-value: 1.74e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24580581  655 TRTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQglNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFGK 729
Cdd:cd12262    3 SRNVYVGNLDDSLTEEEIRGILEKYGEIESIKILKE--KNCAFVNYLNIANAIKAVQELPIKNPKFKKVRINYGK 75
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
 658-728 1.88e-08

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: 54.17  E-value: 1.88e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKK---QGLN-AYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFG 728
Cdd:cd12284    1 LYVGSLHFNITEDMLRGIFEPFGKIEFVQLQKdpeTGRSkGYGFIQFRDAEDAKKALEQLNGFELAGRPMKVGHV 75
RRM_NELFE cd12305
RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This ...
 734-806 6.76e-08

RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif.


Pssm-ID: 409746 [Multi-domain]  Cd Length: 75  Bit Score: 52.71  E-value: 6.76e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24580581  734 NCVWIDGVDekVSESFLQSQFTRFGAVTKVSIDRNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDFASR 806
Cdd:cd12305    5 NTVYVSGYG--ITEDVLKKAFSPFGNIINISMEIEKNCAFVTFEKMESADQAIAELNGTTVEGVQLKVSIARR 75
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 2000-2080 1.23e-07

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 57.24  E-value: 1.23e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   2000 QKEKEIREKDlREKEQRERdNREKELRDKDLREKEMREK-EQREKELHREK---DQREREHR--EKEQSRRAMDVEQEGR 2073
Cdd:pfam13868  161 LKEKAEREEE-REAEREEI-EEEKEREIARLRAQQEKAQdEKAERDELRAKlyqEEQERKERqkEREEAEKKARQRQELQ 238


                   ....*..
gi 24580581   2074 GGRMREL 2080
Cdd:pfam13868  239 QAREEQI 245
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 657-801 1.33e-07

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: 58.28  E-value: 1.33e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    657 TLFIGNLEKDITAGELRSHFEAFGEIIEI----DIKKQGLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFG---- 728
Cdd:TIGR01628    2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVrvcrDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSqrdp 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    729 ---KSMPTNcVWIDGVDEKVSESFLQSQFTRFGAVT--KVSIDRN---RQLALVLYDQVQNAQAAVKDMRGTILRRKKLQ 800
Cdd:TIGR01628   82 slrRSGVGN-IFVKNLDKSVDNKALFDTFSKFGNILscKVATDENgksRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVY 160


                   .
gi 24580581    801 V 801
Cdd:TIGR01628  161 V 161
ARGLU pfam15346
Arginine and glutamate-rich 1; ARGLU, arginine and glutamate-rich 1 protein family, is ...
 2000-2071 1.43e-07

Arginine and glutamate-rich 1; ARGLU, arginine and glutamate-rich 1 protein family, is required for the oestrogen-dependent expression of ESR1 target genes. It functions in cooperation with MED1. The family of proteins is found in eukaryotes.


Pssm-ID: 405931 [Multi-domain]  Cd Length: 151  Bit Score: 53.90  E-value: 1.43e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581   2000 QKEKEIREKDLR-EKEQRERDNREKELRDKDLREKEMREK--EQREKELHREKDQ-REREHREKEQSRRaMDVEQE 2071
Cdd:pfam15346   61 EREAELEEERRKeEEERKKREELERILEENNRKIEEAQRKeaEERLAMLEEQRRMkEERQRREKEEEER-EKREQQ 135
RRM smart00360
RNA recognition motif;
556-627 1.44e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 51.83  E-value: 1.44e-07
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581     556 IRVRNLPARSSDTSLKDgLFheyKKHGKVTWVKVV----GQNSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEV 627
Cdd:smart00360    2 LFVGNLPPDTTEEELRE-LF---SKFGKVESVRLVrdkeTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 736-802 1.48e-07

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: 51.51  E-value: 1.48e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24580581  736 VWIDGVDEKVSESFLQSQFTRFGAVTKVSIDRNRQL-----ALVLYDQVQNAQAAVKDMRGTILRRKKLQVD 802
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGkskgfAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RRM_SNP1_like cd21615
RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ...
 642-717 8.96e-07

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: 50.77  E-value: 8.96e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  642 PYEAELDEYhpkstRTLFIGNLEKDITAGELRSHFEAFGEIIEIDI-------KKQGlnaYAFCQYSDIVSVVKAMRKMD 714
Cdd:cd21615   10 PHIADGDPY-----KTLFVGRLDYSLTELELQKKFSKFGEIEKIRIvrdketgKSRG---YAFIVFKSESDAKNAFKEGN 81


                 ...
gi 24580581  715 GEH 717
Cdd:cd21615   82 GLR 84
RRM_RBM22 cd12224
RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This ...
 656-729 1.22e-06

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: 49.21  E-value: 1.22e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581  656 RTLFIGNLEKDITAGELRSHFEAFGEIIEIDI--KKQglnaYAFCQYSDIVSVVKAMRKMDGEH-LGSNRIKLGFGK 729
Cdd:cd12224    2 TTLYVGGLGDKITEKDLRDHFYQFGEIRSITVvaRQQ----CAFVQFTTRQAAERAAERTFNKLiIKGRRLKVKWGR 74
CAF-1_p150 pfam11600
Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide ...
 1998-2064 1.55e-06

Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesized and acetylated histones H3/H4 into chromatin during DNA replication and repair. CAF-1_p150 includes the HP1 interaction site, the PEST, KER and ED interacting sites. CAF-1_p150 interacts directly with newly synthesized and acetylated histones through the acidic KER and ED domains. The PEST domain is associated with proteins that undergo rapid proteolysis.


Pssm-ID: 402959 [Multi-domain]  Cd Length: 164  Bit Score: 51.61  E-value: 1.55e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1998 KEQKEKEIRE-KDLREKEQRERDNREKELRDKDLREKEMREKEQREKELHR--EKDQREREHREKEQSRR 2064
Cdd:pfam11600   53 KEEARRKKEEeKELKEKERREKKEKDEKEKAEKLRLKEEKRKEKQEALEAKleEKRKKEEEKRLKEEEKR 122
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
 656-727 1.76e-06

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: 48.67  E-value: 1.76e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24580581  656 RTLFIGNLEKDITAGELRSHFEAFGEIIEIDI-------KKQGlnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGF 727
Cdd:cd12398    1 RSVFVGNIPYDATEEQLKEIFSEVGPVVSFRLvtdretgKPKG---YGFCEFRDAETALSAVRNLNGYELNGRPLRVDF 76
MAP7 pfam05672
MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ...
 1999-2087 3.04e-06

MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent.


Pssm-ID: 461709 [Multi-domain]  Cd Length: 153  Bit Score: 50.42  E-value: 3.04e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1999 EQKEKEIREKdlREKEQRERDNREKELRdkdLREKEMREKEQREKELHREKDQREREHR---EKEQSRRAMDVEQEGRGG 2075
Cdd:pfam05672   17 AEKRRQAREQ--REREEQERLEKEEEER---LRKEELRRRAEEERARREEEARRLEEERrreEEERQRKAEEEAEEREQR 91

                           90
                   ....*....|..
gi 24580581   2076 RMRELSSYQKSK 2087
Cdd:pfam05672   92 EQEEQERLQKQK 103
RRM1_SRSF1_like cd12338
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
 657-727 3.06e-06

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: 47.74  E-value: 3.06e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24580581  657 TLFIGNLEKDITAGELRSHFEAFGEIIEIDIKK-QGLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGF 727
Cdd:cd12338    1 RIYVGNLPGDIRERDIEDLFYKYGPILAIDLKNrRRGPPFAFVEFEDPRDAEDAIRGRDGYDFDGYRLRVEF 72
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
 655-732 3.95e-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: 47.66  E-value: 3.95e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  655 TRTLFIGNLEKDITAGELRSHFEAFGEI--IEIDIKKQGlnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFgkSMP 732
Cdd:cd12524    1 SRTLFVRNINSSVEDEELRALFEQFGEIrtLYTACKHRG---FIMVSYYDIRAAQSAKRALQGTELGGRKLDIHF--SIP 75
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
 657-731 4.35e-06

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: 47.53  E-value: 4.35e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  657 TLFIGNLEKDITAGELRSH----FEAFGEIIEIDIKK-QGLNAYAFCQYSDIVSVVKAMRKMDGEHLgsnriklgFGKSM 731
Cdd:cd12246    1 TLYINNLNEKIKKDELKRSlyalFSQFGPVLDIVASKsLKMRGQAFVVFKDVESATNALRALQGFPF--------YGKPM 72
RRM1_VICKZ cd12358
RNA recognition motif 1 (RRM1) found in the VICKZ family proteins; Thid subfamily corresponds ...
 658-725 6.40e-06

RNA recognition motif 1 (RRM1) found in the VICKZ family proteins; Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains.


Pssm-ID: 240804 [Multi-domain]  Cd Length: 73  Bit Score: 46.98  E-value: 6.40e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24580581  658 LFIGNLEKDITAGELRSHF-EAFGEIIEIDIKKQGlnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKL 725
Cdd:cd12358    1 LYIGNLSSDVNESDLRQLFeEHKIPVSSVLVKKGG---YAFVDCPDQSWADKAIEKLNGKILQGKVIEV 66
CAF-1_p150 pfam11600
Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide ...
 1998-2079 6.69e-06

Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesized and acetylated histones H3/H4 into chromatin during DNA replication and repair. CAF-1_p150 includes the HP1 interaction site, the PEST, KER and ED interacting sites. CAF-1_p150 interacts directly with newly synthesized and acetylated histones through the acidic KER and ED domains. The PEST domain is associated with proteins that undergo rapid proteolysis.


Pssm-ID: 402959 [Multi-domain]  Cd Length: 164  Bit Score: 49.69  E-value: 6.69e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1998 KEQKEKEIREKdLREKEQRERDNREKELRDKDLREKEMREKEQREKelhREKDQRER--EHREKEQSRRAmdvEQEGRGG 2075
Cdd:pfam11600   30 KLEAEKEEKER-LKEEAKAEKERAKEEARRKKEEEKELKEKERREK---KEKDEKEKaeKLRLKEEKRKE---KQEALEA 102


                   ....
gi 24580581   2076 RMRE 2079
Cdd:pfam11600  103 KLEE 106
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 1998-2071 7.36e-06

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 51.84  E-value: 7.36e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1998 KEQKEKEIREKDLRE---KEQRERDNREKELRDKDLREKE-----MREKEQREKELHREKDQREREhREKEQSRRAMDVE 2069
Cdd:pfam13868  116 AEAEEKLEKQRQLREeidEFNEEQAEWKELEKEEEREEDErileyLKEKAEREEEREAEREEIEEE-KEREIARLRAQQE 194


                   ..
gi 24580581   2070 QE 2071
Cdd:pfam13868  195 KA 196
RRM3_RBM15B cd12558
RNA recognition motif 3 (RRM3) found in putative RNA-binding protein 15B (RBM15B) from ...
 732-805 7.69e-06

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: 46.93  E-value: 7.69e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581  732 PTNCVWIDGVDEKVSESFLQSQFTRFGAVTKVSIDRNRQLALVLYDQVQNAQAAVKDMRGTIL--RRKKLQVDFAS 805
Cdd:cd12558    1 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDYVKGDSFAYIQYESLDAAQAACAQMRGFPLggPDRRLRVDFAK 76
DDRGK pfam09756
DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and ...
 2003-2104 7.84e-06

DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif.


Pssm-ID: 370664 [Multi-domain]  Cd Length: 188  Bit Score: 50.04  E-value: 7.84e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   2003 KEIREKDLREKEQRERDNREKELRDkdlREKEMREK--EQREKELHREKDQREREHREKEQSRRAMDVEQEgrggrMREL 2080
Cdd:pfam09756    1 KKLGAKKRAKLELKEAKRQQREAEE---EEREEREKleEKREEEYKEREEREEEAEKEKEEEERKQEEEQE-----RKEQ 72

                           90       100
                   ....*....|....*....|....
gi 24580581   2081 SSYQKSKMDIAGEASSLTAIDCQH 2104
Cdd:pfam09756   73 EEYEKLKSQFVVEEEGTDKLSAED 96
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
 657-728 1.05e-05

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: 46.12  E-value: 1.05e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24580581  657 TLFIGNLEKDITAGELRSHFEAFGEIIEIDI-KKQGlnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFG 728
Cdd:cd12354    2 TVYVGNITKGLTEALLQQTFSPFGQILEVRVfPDKG---YAFIRFDSHEAATHAIVSVNGTIINGQAVKCSWG 71
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
 658-724 1.07e-05

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: 1.07e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQglnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRIK 724
Cdd:cd12343    2 IFVGNLPDAATSEELRALFEKYGKVTECDIVKN----YAFVHMEKEEDAEDAIKALNGYEFMGSRIN 64
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 3577-3804 1.44e-05

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 51.69  E-value: 1.44e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   3577 PTASQNAMPQASTPKQGPITPQQAIRTQSLIMQPPTISIPEQTPHFAVPQmvlSPQSHHPQQPGTYMVGIRAPSPHSPLH 3656
Cdd:pfam03154  184 PSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQ---TPTLHPQRLPSPHPPLQPMTQPPPPSQ 260

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   3657 SPGRGVAQSRLVGQLSPVGRPMVSQPSPQQQVQQTQQQHALITSPQsSNISPLASPTTRVLSSSNS---PTTSKVNSYQP 3733
Cdd:pfam03154  261 VSPQPLPQPSLHGQMPPMPHSLQTGPSHMQHPVPPQPFPLTPQSSQ-SQVPPGPSPAAPGQSQQRIhtpPSQSQLQSQQP 339

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581   3734 RNQQvPQQPSPKSVAEVQTTPqlmTIPLQKMTPIQVPHHPTIISKVVTVQpqqaTQSQVASSP---PLGSLPPH 3804
Cdd:pfam03154  340 PREQ-PLPPAPLSMPHIKPPP---TTPIPQLPNPQSHKHPPHLSGPSPFQ----MNSNLPPPPalkPLSSLSTH 405
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
655-724 1.51e-05

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 46.24  E-value: 1.51e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581  655 TRTLFIGNLEKDITAGELRSHFEAFGEIIEIDI-------KKQGlnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRIK 724
Cdd:COG0724    1 SMKIYVGNLPYSVTEEDLRELFSEYGEVTSVKLitdretgRSRG---FGFVEMPDDEEAQAAIEALNGAELMGRTLK 74
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
 658-715 1.72e-05

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: 45.80  E-value: 1.72e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDI-------KKQGLnayAFCQYSDIVSVVKAMRKMDG 715
Cdd:cd12316    2 LFVRNLPFTATEDELRELFEAFGKISEVHIpldkqtkRSKGF---AFVLFVIPEDAVKAYQELDG 63
RRM2_TDP43 cd12322
RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar ...
 656-702 1.78e-05

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: 45.77  E-value: 1.78e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24580581  656 RTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQgLNAYAFCQYSD 702
Cdd:cd12322    1 RKVFVGRCTEDMTEDDLRQYFSQFGEVTDVFIPKP-FRAFAFVTFAD 46
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 1940-2071 1.90e-05

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 50.69  E-value: 1.90e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1940 KQVEREEKDRKAQQEErekedrkakeeekererekkaqedrekkereerelrekeqrDKEQKEKEIreKDLREKEQRERD 2019
Cdd:pfam13868  162 KEKAEREEEREAEREE-----------------------------------------IEEEKEREI--ARLRAQQEKAQD 198

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24580581   2020 NREK--ELR--------DKDLREKEMREKEQREKELHREKDQREREHREKEQsRRAMDVEQE 2071
Cdd:pfam13868  199 EKAErdELRaklyqeeqERKERQKEREEAEKKARQRQELQQAREEQIELKER-RLAEEAERE 259
RRM1_CoAA cd12608
RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator ...
 658-723 2.00e-05

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: 45.56  E-value: 2.00e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQglnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRI 723
Cdd:cd12608    3 IFVGNVDEDTSQEELSALFEPYGAVLSCAVMKQ----FAFVHMRGEAAADRAIRELNGRELHGRAL 64
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 1997-2073 2.19e-05

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 50.30  E-value: 2.19e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24580581   1997 DKEQKEkEIREKdlREKEQRERDNREKELRDKDLREKEMRE-KEQREKELHREKDQRERE-HREKEQSRRAMDVEQEGR 2073
Cdd:pfam13868  199 EKAERD-ELRAK--LYQEEQERKERQKEREEAEKKARQRQElQQAREEQIELKERRLAEEaEREEEEFERMLRKQAEDE 274
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
 655-730 2.32e-05

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: 45.75  E-value: 2.32e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  655 TRTLFIGNLEKDITAGELRSHFEAFGEIIEIDI---------KKQGLNAY-AFCQYSDivsVVKAMRKMDGEHLGSNRIK 724
Cdd:cd12223    1 TTNLYVGNLPPSVTEEVLLREFGRFGPLASVKImwprteeerRRNRNCGFvAFMSRAD---AERAMRELNGKDVMGYELK 77


                 ....*.
gi 24580581  725 LGFGKS 730
Cdd:cd12223   78 LGWGKA 83
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
 657-725 2.46e-05

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: 45.68  E-value: 2.46e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581  657 TLFIGNLEKDITAGELRSHFEAFGEIIEIDI------KKQGLNA-YAFCQYSDIVSVVKAMRKMDGEHLGSNRIKL 725
Cdd:cd12318    2 TLFVKNLNFKTTEEALKKHFEKCGPIRSVTIakkkdpKGPLLSMgYGFVEFKSPEAAQKALKQLQGTVLDGHALEL 77
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
 658-724 3.35e-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: 44.93  E-value: 3.35e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQ--GlnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRIK 724
Cdd:cd12373    2 VYVGNLGPRVTKRELEDAFEKYGPLRNVWVARNppG---FAFVEFEDPRDAEDAVRALDGRRICGSRVR 67
RRM2_RBM4 cd12607
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup ...
 658-723 3.65e-05

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: 44.57  E-value: 3.65e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQglnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRI 723
Cdd:cd12607    3 LHVGNISSSCTNQELRAKFEEYGPVIECDIVKD----YAFVHMERAEDAMEAIRGLDNTEFQGKRM 64
RRM1_RIM4_like cd12453
RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; ...
 558-629 3.75e-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: 45.09  E-value: 3.75e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24580581  558 VRNLPARSSDTSLKDGLFHEYKKHGKVTWVKVVGQNSER-YALVCFKKPDDVEKALEVSHDKHFFGCKIEVEP 629
Cdd:cd12453    7 VASLSSARSDEELCAAVTNHFSKWGELLNVKVLKDWSNRpYAFVQYTNTEDAKNALVNGHNTLLDGRHLRVEK 79
RRM2_SREK1 cd12260
RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 ...
 656-724 4.36e-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: 44.99  E-value: 4.36e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24580581  656 RTLFIGNLEKDITAGELRSHFEAFGEI--IEIDIKKQGLNAYAFCQYSDIVSVVKAMrKMDGEHLGSNRIK 724
Cdd:cd12260    5 RTVYVGNLDPSTTADQLLEFFSQAGEVkyVRMAGDETQPTRYAFVEFAEQTSVINAL-KLNGKMFGGRPLK 74
RRM1_HRB1_GBP2 cd21605
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, ...
 657-717 4.93e-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: 44.59  E-value: 4.93e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581  657 TLFIGNLEKDITAGELRSHFEAFGEIIEIDI-----KKQGLNAYAFcqySDIVSVVKAMRKMDGEH 717
Cdd:cd21605    3 SIFVGNLPFDCTWEDLKDHFSQVGEVIRADIvtsrgRHRGMGTVEF---TNKEDVDRAISKFDHTM 65
RRM3_RBM15 cd12557
RNA recognition motif 3 (RRM3) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
 736-804 5.25e-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: 44.54  E-value: 5.25e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24580581  736 VWIDGVDEKVSESFLQSQFTRFGAVTKVSIDRNRQLALVLYDQVQNAQAAVKDMRGTIL--RRKKLQVDFA 804
Cdd:cd12557    2 LWVGGLGPWVPLAALAREFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLggPDRRLRVDFA 72
RRM_PPARGC1A_like cd12357
RNA recognition motif (RRM) found in the peroxisome proliferator-activated receptor gamma ...
 656-700 5.43e-05

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: 45.11  E-value: 5.43e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24580581  656 RTLFIGNLEKDITAGELRSHFEAFGEIIEIDI--KKQGLNaYAFCQY 700
Cdd:cd12357    3 RVVYVGKLEQDTTRSELRRRFEVFGEIEECTVhfRERGDK-YGFVTY 48
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage ...
 653-725 7.21e-05

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup 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.


Pssm-ID: 410072 [Multi-domain]  Cd Length: 85  Bit Score: 44.43  E-value: 7.21e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  653 KSTRTLFIGNLEKDITAGELRSHFEAFGEIIEIDI-------KKQGlnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKL 725
Cdd:cd12671    4 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLvydretgKPKG---YGFCEYQDQETALSAMRNLNGYELNGRALRV 80
DUF4659 pfam15558
Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins ...
 1997-2084 7.73e-05

Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins in this family are typically between 427 and 674 amino acids in length. There are two completely conserved residues (D and I) that may be functionally important.


Pssm-ID: 464768 [Multi-domain]  Cd Length: 374  Bit Score: 48.88  E-value: 7.73e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1997 DKEQKEKEIREKDL----------REKEQR-ERDNREKElRDKDLREKEMREKEQREKELHREKDQREREH--------- 2056
Cdd:pfam15558   41 DQKRQETLERERRLllqqsqeqwqAEKEQRkARLGREER-RRADRREKQVIEKESRWREQAEDQENQRQEKlerarqeae 119

                           90       100       110
                   ....*....|....*....|....*....|.
gi 24580581   2057 ---REKEQSRRamdvEQEGRGGRMRELSSYQ 2084
Cdd:pfam15558  120 qrkQCQEQRLK----EKEEELQALREQNSLQ 146
RRM1_p54nrb_like cd12332
RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
 658-715 8.50e-05

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: 43.82  E-value: 8.50e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQglNAYAFCQYSDIVSVVKAMRKMDG 715
Cdd:cd12332    4 LFVGNLPNDITEEEFKELFQKYGEVSEVFLNKG--KGFGFIRLDTRANAEAAKAELDG 59
MAP7 pfam05672
MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ...
 1938-2059 8.51e-05

MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent.


Pssm-ID: 461709 [Multi-domain]  Cd Length: 153  Bit Score: 46.19  E-value: 8.51e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1938 LRKQVEREEKDRKAQQEEREKEDRKAKEEEKERErekkaQEDREKKEREERELREKEQRDKEQKEKEIREKDLREKEQRE 2017
Cdd:pfam05672   23 AREQREREEQERLEKEEEERLRKEELRRRAEEER-----ARREEEARRLEEERRREEEERQRKAEEEAEEREQREQEEQE 97

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 24580581   2018 RDNREKElrDKDLREKEMREKEQREKELHREKDQREREHREK 2059
Cdd:pfam05672   98 RLQKQKE--EAEAKAREEAERQRQEREKIMQQEEQERLERKK 137
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
 657-723 8.55e-05

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: 43.70  E-value: 8.55e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24580581  657 TLFIGNLEKDITAGELRSHFEAFGEIIEIDI---KKQGLN-AYAFCQYSDIVSVVKAMRKMDGEHLGSNRI 723
Cdd:cd21608    1 KLYVGNLSWDTTEDDLRDLFSEFGEVESAKVitdRETGRSrGFGFVTFSTAEAAEAAIDALNGKELDGRSI 71
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
 658-724 8.67e-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: 43.76  E-value: 8.67e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIE----IDIKKQGLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIK 724
Cdd:cd12362    1 LFVYHLPNEFTDQDLYQLFAPFGNVVSakvfVDKNTGRSKGFGFVSYDNPLSAQAAIKAMNGFQVGGKRLK 71
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 1998-2080 1.01e-04

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 48.38  E-value: 1.01e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1998 KEQKEKEIREKDLREKE-QRERDNREKELRDKdlREKEMREKEQREKELHR--EKDQREREHREKEQSRRAMDvEQEgRG 2074
Cdd:pfam13868  143 KELEKEEEREEDERILEyLKEKAEREEEREAE--REEIEEEKEREIARLRAqqEKAQDEKAERDELRAKLYQE-EQE-RK 218


                   ....*.
gi 24580581   2075 GRMREL 2080
Cdd:pfam13868  219 ERQKER 224
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
 658-724 1.07e-04

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: 43.75  E-value: 1.07e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDI----KKQGLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIK 724
Cdd:cd12347    1 LYVGGLAEEVDEKVLHAAFIPFGDIVDIQIpldyETEKHRGFAFVEFEEAEDAAAAIDNMNESELFGRTIR 71
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
 558-627 1.12e-04

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: 43.39  E-value: 1.12e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  558 VRNLPARSSDTSLKDglfhEYKKHGKVTWVKVVgqnsERYALVCFKKPDDVEKALEVSHDKHFFGCKIEV 627
Cdd:cd12251    6 VRNLMLSTTEEKLRE----LFSEYGKVERVKKI----KDYAFVHFEERDDAVKAMEEMNGKELEGSEIEV 67
RRM_RBM8 cd12324
RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; ...
 737-804 1.16e-04

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: 43.75  E-value: 1.16e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581  737 WI---DGVDEKVSESFLQSQFTRFGAVT--KVSIDRN----RQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDFA 804
Cdd:cd12324    7 WIifvTGVHEEAQEEDIHDKFAEFGEIKnlHLNLDRRtgfvKGYALVEYETKKEAQAAIEGLNGKELLGQTISVDWA 83
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 1938-2079 1.18e-04

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 47.99  E-value: 1.18e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1938 LRKQVEREeKDRKAQQEE----REKEDRKAKEEekererekkaqedrekkereerelrekeQRDKEQKEKEI-------- 2005
Cdd:pfam13868  189 LRAQQEKA-QDEKAERDElrakLYQEEQERKER----------------------------QKEREEAEKKArqrqelqq 239

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   2006 -REKDLREKE---QRERDnREKELRDKDLRE-KEMREKEQREKELHREKDQREREH-----REKEQSRRA--MDVEQEGR 2073
Cdd:pfam13868  240 aREEQIELKErrlAEEAE-REEEEFERMLRKqAEDEEIEQEEAEKRRMKRLEHRRElekqiEEREEQRAAerEEELEEGE 318


                   ....*.
gi 24580581   2074 GGRMRE 2079
Cdd:pfam13868  319 RLREEE 324
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
 658-697 1.21e-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: 43.33  E-value: 1.21e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDI---KKQGLNAYAF 697
Cdd:cd12226    2 LFVGGLSPSITEDDLERRFSRFGTVSDVEIirkKDAPDRGFAY 44
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
 655-793 1.24e-04

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: 48.01  E-value: 1.24e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    655 TRTLFIGN-LEKDITAGELRSHFEAFGEI-----IEIDIKKQGLnAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFG 728
Cdd:TIGR01661    2 SKTNLIVNyLPQTMTQEEIRSLFTSIGEIescklVRDKVTGQSL-GYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24580581    729 K----SMPTNCVWIDGVDEKVSESFLQSQFTRFGAVTKVSI------DRNRQLALVLYDQVQNAQAAVKDMRGTI 793
Cdd:TIGR01661   81 RpssdSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRIlsdnvtGLSKGVGFIRFDKRDEADRAIKTLNGTT 155
RRM1_PUB1 cd12614
RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated ...
 658-725 1.31e-04

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: 43.19  E-value: 1.31e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEI----IEIDIKKQGLNaYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKL 725
Cdd:cd12614    1 LYVGNLDPRVTEDLLQEIFAVTGPVenckIIPDKNSKGVN-YGFVEYYDRRSAEIAIQTLNGRQIFGQEIKV 71
MAP7 pfam05672
MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ...
 1998-2079 1.36e-04

MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent.


Pssm-ID: 461709 [Multi-domain]  Cd Length: 153  Bit Score: 45.42  E-value: 1.36e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1998 KEQKEKE-IREKDLREKEQRERDNREKELRdkDLREKEMREKEQREKElhREKDQREREHREKEQSRRaMDVEQEGRGGR 2076
Cdd:pfam05672   35 LEKEEEErLRKEELRRRAEEERARREEEAR--RLEEERRREEEERQRK--AEEEAEEREQREQEEQER-LQKQKEEAEAK 109


                   ...
gi 24580581   2077 MRE 2079
Cdd:pfam05672  110 ARE 112
RRM_RBMX_like cd12382
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y ...
 736-806 1.55e-04

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: 43.16  E-value: 1.55e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581  736 VWIDGVDEKVSESFLQSQFTRFGAVTKVSI------DRNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDFASR 806
Cdd:cd12382    4 LFIGGLNTETNEKALEAVFGKYGRIVEVLLmkdretNKSRGFAFVTFESPADAKDAARDMNGKELDGKAIKVEQATK 80
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
 657-729 1.57e-04

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: 42.82  E-value: 1.57e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  657 TLFIGNLEKD-ITAGELRSHFEAFGEIIEIDIKKQglnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFGK 729
Cdd:cd12233    1 TLFVVGFDPGtTREEDIEKLFEPFGPLVRCDIRKT----FAFVEFEDSEDATKALEALHGSRIDGSVLTVEFVK 70
RRM2_SRSF1_4_like cd12339
RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF4 and ...
 556-628 1.65e-04

RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins; This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of 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). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising 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. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It 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 with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409776 [Multi-domain]  Cd Length: 70  Bit Score: 42.96  E-value: 1.65e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24580581  556 IRVRNLPARSSDTSLKDGLfheyKKHGKVTWVKVVGQNsERYALVCFKKPDDVEKALEVSHDKHFFGCKIEVE 628
Cdd:cd12339    3 VVVSNLPERASWQDLKDFM----RKAGEVTYADVHRDR-EGEGVVEFTSEEDMKRAIEKLDGTEFNGRRIRVE 70
RRM2_TIA1_like cd12353
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and ...
 658-724 1.72e-04

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: 43.15  E-value: 1.72e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDI-------KKQGlnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRIK 724
Cdd:cd12353    2 IFVGDLSPEIETEDLKEAFAPFGEISDARVvkdtqtgKSKG---YGFVSFVKKEDAENAIQGMNGQWLGGRNIR 72
ERM_helical pfam20492
Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ...
 2000-2080 1.79e-04

Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins.


Pssm-ID: 466641 [Multi-domain]  Cd Length: 120  Bit Score: 44.14  E-value: 1.79e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   2000 QKEKEIREKDLRE--------KEQRERDNREKELRDKDLRE-KEMREKEQREKEL-HREKDQREREHREKEQSRRAMDVE 2069
Cdd:pfam20492   19 EEETKKAQEELEEseetaeelEEERRQAEEEAERLEQKRQEaEEEKERLEESAEMeAEEKEQLEAELAEAQEEIARLEEE 98

                           90
                   ....*....|.
gi 24580581   2070 QEGRGGRMREL 2080
Cdd:pfam20492   99 VERKEEEARRL 109
RRM3_hnRNPR cd12494
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R ...
 656-729 1.95e-04

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: 42.71  E-value: 1.95e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  656 RTLFIGNLEKDITAGELRSHFEAFGEIIEIdiKKqgLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFGK 729
Cdd:cd12494    2 KVLFVRNLATTVTEEILEKTFSQFGKLERV--KK--LKDYAFVHFEDRDAAVKAMDEMNGKEVEGEEIEIVLAK 71
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
 656-723 2.06e-04

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: 43.02  E-value: 2.06e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24580581  656 RTLFIGNLEKDITAGELRSHFEAFGEIIEIDI-----KKQGL--NAYAFCQYSDIVSVVKAMrKMDGEHLGSNRI 723
Cdd:cd12298    1 REIRVRNLDFELDEEALRGIFEKFGEIESINIpkkqkNRKGRhnNGFAFVTFEDADSAESAL-QLNGTLLDNRKI 74
RRM1_MEI2_EAR1_like cd12275
RNA recognition motif 1 (RRM1) found in Mei2-like proteins and terminal EAR1-like proteins; ...
 655-727 2.11e-04

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: 42.55  E-value: 2.11e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24580581  655 TRTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQGlNAYAFCQYSDIVSVVKAMRKMDGEHLgSNRIKLGF 727
Cdd:cd12275    1 SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERIS-EGIVTVHFYDIRDAKRAVRELCGRHM-QQQALGGS 71
RRM_SCAF4_SCAF8 cd12227
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), ...
 655-725 2.25e-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: 42.81  E-value: 2.25e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24580581  655 TRTLFIGNLEKDITAGELRSHFEAFGEIIEID-IKKQGLnayAFCQYSDIVSVVKAMRKMDGEHLGSNRIKL 725
Cdd:cd12227    2 STTLWVGHLSKKVTQEELKNLFEEYGEIQSIDmIPPRGC---AYVCMKTRQDAHRALQKLKNHKLRGKSIKI 70
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 3483-3797 2.37e-04

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: 47.99  E-value: 2.37e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   3483 PSVITKLPFLDT-----PKTVpAGLPPS---PVKIEPPTISKlqqPLVQPVQTVLPAPHSTGSGISANSVINLDLSNVIS 3554
Cdd:pfam05109  425 PESTTTSPTLNTtgfaaPNTT-TGLPSSthvPTNLTAPASTG---PTVSTADVTSPTPAGTTSGASPVTPSPSPRDNGTE 500

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   3555 SCSNTSAASATASASASISFGSPT-ASQNAMPQASTPKQGPITPQQAIRTQSLIMQPPTISIPEQTPHFAVPQM-VLSPQ 3632
Cdd:pfam05109  501 SKAPDMTSPTSAVTTPTPNATSPTpAVTTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPTPNATIPTLgKTSPT 580

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   3633 ShhpqqpgtymvGIRAPSPHsplhspgrgvAQSRLVGQLSPvgrpmvsqpspqqqvQQTQQQHAL-ITSPQSSNISPLAS 3711
Cdd:pfam05109  581 S-----------AVTTPTPN----------ATSPTVGETSP---------------QANTTNHTLgGTSSTPVVTSPPKN 624

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   3712 PTTRVLSSSNSPTTSKVNSYQPRNQQVPQQPSPkSVAEVQTTpqlmtiplqkMTPIQVPHHPTIISKVVTVQPQQATQSQ 3791
Cdd:pfam05109  625 ATSAVTTGQHNITSSSTSSMSLRPSSISETLSP-STSDNSTS----------HMPLLTSAHPTGGENITQVTPASTSTHH 693


                   ....*.
gi 24580581   3792 VASSPP 3797
Cdd:pfam05109  694 VSTSSP 699
RRM_G3BP cd12229
RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, ...
 658-713 2.49e-04

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: 42.79  E-value: 2.49e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQGLNA----YAFCQYSDIVSVVKAMRKM 713
Cdd:cd12229    6 LFVGNLPHDITEDELKEFFSRFGNVLELRINSKGGGGrlpnFGFVVFDDPEAVQKILANK 65
RRM_Nop6 cd12400
RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ...
 658-723 2.77e-04

RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins; This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing.


Pssm-ID: 409834 [Multi-domain]  Cd Length: 74  Bit Score: 42.21  E-value: 2.77e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDI-------KKQGlnaYAFCQYSDIVSVVKAMrKMDGEHLGSNRI 723
Cdd:cd12400    3 LFVGNLPYDTTAEDLKEHFKKAGEPPSVRLltdkktgKSKG---CAFVEFDNQKALQKAL-KLHHTSLGGRKI 71
RRM2_MRN1 cd12523
RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This ...
 654-729 2.93e-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: 42.42  E-value: 2.93e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581  654 STRTLFIGNLEKDITAGELRSHFEAFGEIIEIDI-KKQGLnayAFCQYSDIVSVVKAMRKMDGEHLGSNRiKLGFGK 729
Cdd:cd12523    2 ASRNVYLGNLPESITEEELREDLEKFGPIDQIKIvKEKNI---AFVHFLSIANAIKVVTTLPLNPKWAKR-RIYYGK 74
RRM1_hnRNPA_hnRNPD_like cd12325
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and ...
 658-717 4.04e-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: 41.74  E-value: 4.04e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQGLN----AYAFCQYSDIVSVVKAMRkmDGEH 717
Cdd:cd12325    1 LFVGGLSWETTEESLREYFSKYGEVVDCVVMKDPATgrsrGFGFVTFKDPSSVDAVLA--ARPH 62
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
 658-727 4.12e-04

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: 42.12  E-value: 4.12e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEI----IEIDIKKQGLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGF 727
Cdd:cd12399    1 LYVGNLPYSASEEQLKSLFGQFGAVfdvkLPMDRETKRPRGFGFVELQEEESAEKAIAKLDGTDFMGRTIRVNE 74
sex-lethal TIGR01659
sex-lethal family splicing factor; This model describes the sex-lethal family of splicing ...
 648-793 4.72e-04

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: 46.16  E-value: 4.72e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    648 DEYHPKSTRTLFIGN-LEKDITAGELRSHFEAFGEI----IEIDIKKQGLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNR 722
Cdd:TIGR01659   99 DDNDTNNSGTNLIVNyLPQDMTDRELYALFRTIGPIntcrIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKR 178

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    723 IKLGF----GKSMPTNCVWIDGVDEKVSESFLQSQFTRFGAVTKVSIDRN------RQLALVLYDQVQNAQAAVKDMRGT 792
Cdd:TIGR01659  179 LKVSYarpgGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDkltgtpRGVAFVRFNKREEAQEAISALNNV 258


                   .
gi 24580581    793 I 793
Cdd:TIGR01659  259 I 259
RRM3_Spen cd12310
RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily ...
 658-729 4.81e-04

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: 41.50  E-value: 4.81e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQglNAYAFCQYSDIVSVVKAMRKMDGEHLGSN--RIKLGFGK 729
Cdd:cd12310    1 LWVGGLGPWTSLAELEREFDRFGAIRKIDYRKG--DDYAYILYESLDAAQAAVRALRGFPLGGPdrRLRVDFAD 72
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
 656-723 4.86e-04

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: 42.22  E-value: 4.86e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24580581  656 RTLFIGNLEKDITAGELRSHFEAFGEIIEI----DIKKQGLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRI 723
Cdd:cd12236    2 KTLFVARLSYDTTESKLRREFEKYGPIKRVrlvrDKKTGKSRGYAFIEFEHERDMKAAYKHADGKKIDGRRV 73
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 744-804 5.15e-04

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: 41.77  E-value: 5.15e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581  744 KVSESFLQSQFTRFGAVTKVSIDRN-----RQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDFA 804
Cdd:cd12414   10 KCTEDDLKKLFSKFGKVLEVTIPKKpdgklRGFAFVQFTNVADAAKAIKGMNGKKIKGRPVAVDWA 75
RRM3_hnRNPQ cd12495
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q ...
 656-729 5.30e-04

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: 41.51  E-value: 5.30e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  656 RTLFIGNLEKDITAGELRSHFEAFGEIIEIdiKKqgLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFGK 729
Cdd:cd12495    2 KVLFVRNLANTVTEEILEKAFSQFGKLERV--KK--LKDYAFIHFDERDGAVKAMDEMNGKDLEGENIEIVFAK 71
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
 556-628 5.70e-04

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: 41.39  E-value: 5.70e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581  556 IRVRNLPARSSDTSLKDglfhEYKKHGKVTWVKVV---GQNSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEVE 628
Cdd:cd12565    3 IIVKNLPKYVTEKRLKE----HFSKKGEITDVKVMrtkDGKSRRFGFIGFKSEEEAQKAVKYFNKTFIDTSKISVE 74
RRM2_RBM34 cd12395
RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
 657-719 6.13e-04

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409829 [Multi-domain]  Cd Length: 73  Bit Score: 41.33  E-value: 6.13e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581  657 TLFIGNLEKDITAGELRSHFEAFGEIIEIDI---KKQGLN-AYAFCQYSDIVSVVKAMrKMDGEHLG 719
Cdd:cd12395    1 SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIvrdRETGIGkGFGYVLFKDKDSVDLAL-KLNGSKLR 66
RRM1_2_CID8_like cd12225
RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting ...
 656-730 6.84e-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: 41.29  E-value: 6.84e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581  656 RTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQGLNA-YAFCQYSDIVSVVKAMRKmDGEHLGSNRIKLGFGKS 730
Cdd:cd12225    1 RTIHVGGIDGSLSEDELADYFSNCGEVTQVRLCGDRVHTrFAWVEFATDASALSALNL-DGTTLGGHPLRVSPSKT 75
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
 658-723 6.94e-04

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: 41.09  E-value: 6.94e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDI----KKQGLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRI 723
Cdd:cd12417    2 LWISGLSDTTKAADLKKIFSKYGKVVSAKVvtsaRTPGSRCYGYVTMASVEEADLCIKSLNKTELHGRVI 71
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 1939-2086 7.65e-04

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 46.27  E-value: 7.65e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1939 RKQVEREEKDRKAQQEEREKEDRKAKEEEKEREREKKAQEDREKKEREERELREKEQRDKEQKEKE---IREKDLREKEQ 2015
Cdd:pfam17380  382 RLQMERQQKNERVRQELEAARKVKILEEERQRKIQQQKVEMEQIRAEQEEARQREVRRLEEERAREmerVRLEEQERQQQ 461

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24580581   2016 RERDNREKELRDkdlREKEMREKEQREKELHREKDQREREhREKEQSRRAMDVEQEGRGGRMRELSSYQKS 2086
Cdd:pfam17380  462 VERLRQQEEERK---RKKLELEKEKRDRKRAEEQRRKILE-KELEERKQAMIEEERKRKLLEKEMEERQKA 528
RRM1_hnRNPA_like cd12578
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
 658-722 7.69e-04

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM1 in 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: 409992 [Multi-domain]  Cd Length: 78  Bit Score: 41.27  E-value: 7.69e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEI----DIKKQGLNAYAFCQYSDIVSVVKAMR----KMDGEHLGSNR 722
Cdd:cd12578    2 LFIGGLSYETTDDSLRNHFEQWGEITDVvvmkDPATKRSRGFGFVTYSSASEVDAAMNarphKVDGRVVEPKR 74
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
 656-729 8.15e-04

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: 41.08  E-value: 8.15e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  656 RTLFIGNLEKDITAGELRSHFEAFGEIIEIdiKKqgLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFGK 729
Cdd:cd12251    2 KVLYVRNLMLSTTEEKLRELFSEYGKVERV--KK--IKDYAFVHFEERDDAVKAMEEMNGKELEGSEIEVSLAK 71
RRM_RBM25 cd12446
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; ...
 656-730 8.33e-04

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor.


Pssm-ID: 409880 [Multi-domain]  Cd Length: 83  Bit Score: 41.36  E-value: 8.33e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24580581  656 RTLFIGNLEKDITAGELRSHFEAFGEIIE----IDIKKQGLNaYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFGKS 730
Cdd:cd12446    1 TTVFVGNIPDDVSDDFIRQLLEKCGKVLSwkrvQDPSGKLKA-FGFCEFEDPEGALRALRLLNGLELGGKKLLVKVDAK 78
RRM1_SRSF1 cd12597
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
 658-727 8.46e-04

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: 41.37  E-value: 8.46e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIK-KQGLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGF 727
Cdd:cd12597    7 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKnRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF 77
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 1992-2088 8.98e-04

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 45.29  E-value: 8.98e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1992 EKEQRDKEQKE--KEIREKDLREKEQRERDNREKELRDKDLR------EKEMREKEQREKELHREKDQREREHRE-KEQS 2062
Cdd:pfam13868   67 RKEERKRYRQEleEQIEEREQKRQEEYEEKLQEREQMDEIVEriqeedQAEAEEKLEKQRQLREEIDEFNEEQAEwKELE 146

                           90       100
                   ....*....|....*....|....*.
gi 24580581   2063 RRAMDVEQEgrggRMRElssYQKSKM 2088
Cdd:pfam13868  147 KEEEREEDE----RILE---YLKEKA 165
RRM2_TatSF1_like cd12282
RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar ...
 570-632 9.71e-04

RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins; This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well.


Pssm-ID: 409724 [Multi-domain]  Cd Length: 91  Bit Score: 41.46  E-value: 9.71e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24580581  570 LKDGLFHEYKKHGKVTWVKVVGQNSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEVEPYQG 632
Cdd:cd12282   25 IKEDLREECEKFGQVKKVVVFDRHPDGVASVKFKEPEEADKCIQALNGRWFAGRKLEAETWDG 87
RRM1_RBM4 cd12606
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup ...
 658-713 1.14e-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: 40.56  E-value: 1.14e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQglnaYAFCQYSDIVSVVKAMRKM 713
Cdd:cd12606    3 LFIGNLPREATEEEIRSLFEQYGKVTECDIIKN----YGFVHMEDKSAADEAIRNL 54
RRM2_MEI2_like cd12529
RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to ...
 657-725 1.24e-03

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: 40.57  E-value: 1.24e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24580581  657 TLFIGNLEKDITAGELRSHFEAFGEIIEIdikKQGLNA--YAFCQYSDIVSVVKAMRKMDGEHLGSNRIKL 725
Cdd:cd12529    3 TLVVFNLDPSISNDDLHQIFGAYGEIKEI---RETPNKrhHKFIEFYDVRSAEAALKALNKSEIAGKRIKL 70
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
 754-801 1.28e-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: 40.73  E-value: 1.28e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 24580581  754 FTRFGAVTKVSIDRNRQ------LALVLYDQVQNAQAAVKDMRGTILRRKKLQV 801
Cdd:cd12393   22 FSKYGKVVKVTILKDKEtrkskgVAFVLFLDRESAHNAVRAMNNKELFGRTLKC 75
RRM1_RBM34 cd12394
RNA recognition motif 1 (RRM1) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
 656-718 1.29e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409828 [Multi-domain]  Cd Length: 91  Bit Score: 41.04  E-value: 1.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  656 RTLFIGNLEKDITAGELRSHFEAFGEIIEIDI-----------------------KKQGLNAYAFcqYSDIVSVVKA--- 709
Cdd:cd12394    1 RTVFVGNLPVTVKKKALKKLFKEFGKIESVRFrsvavanpklpkkvavikkkfhpKRDSMNAYVV--FKEEESAQKAlkl 78

                         90
                 ....*....|
gi 24580581  710 -MRKMDGEHL 718
Cdd:cd12394   79 nGTEFEGHHI 88
RRM2_RIM4_like cd12454
RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins; ...
 655-711 1.29e-03

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: 40.53  E-value: 1.29e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 24580581  655 TRTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQ--GLNAYAFCQYSDIVSVVKAMR 711
Cdd:cd12454    3 KLSIFVGQLDPKTTDSELFRRFSKYGKIVDCKLIKRpePVNAFAFLRFESEEAAEAAVE 61
RRM2_MEI2_EAR1_like cd12276
RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; ...
 657-725 1.33e-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: 40.32  E-value: 1.33e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24580581  657 TLFIGNLEKDITAGELRSHFEAFGEIIEI----DIKKQglnayAFCQYSDIVSVVKAMRKMDGEHLGSNRIKL 725
Cdd:cd12276    3 TLLVFNLDAPVSNDELKSLFSKFGEIKEIrptpDKPSQ-----KFVEFYDVRDAEAALDGLNGRELLGGKLKV 70
SPOC_FPA-like cd21546
SPOC (Spen paralog and ortholog C-terminal) domain found in Arabidopsis thaliana flowering ...
 5376-5515 1.44e-03

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: 41.89  E-value: 1.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 5376 MWQGLLAlKTDQ--AAVQMHFVHGNPNVARASLPslvetntPLLRIAQRmrleqTQLEGVAKKMQVDKEhCMLLALPCGR 5453
Cdd:cd21546    1 KWSGTLA-KSGKprCNVVAHPVSGDVAREPVSLP-------EVLNVSHR-----TDLEEVAHKPVARAV-LVLLFAPENE 66

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24580581 5454 DHADVLQhsrnlqtGFITYLQQKMAAGIVNIPipgseqAAYVVHIFPSCDFANENLERAAPD 5515
Cdd:cd21546   67 SDRGAFD-------EFIDYLSSKDRAGVVKLP------DNRTLYLVPPSEELFSQLLLNVIR 115
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
 655-717 1.44e-03

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: 40.48  E-value: 1.44e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581  655 TRTLFIGNLEKDITAGELRSHFEAFGEIIE----IDIKKQGLNAYAFCQYSDIVSVVKAMRKMDGEH 717
Cdd:cd12566    2 TGRLFLRNLPYSTKEDDLQKLFSKFGEVSEvhvpIDKKTKKSKGFAYVLFLDPEDAVQAYNELDGKV 68
RRM_PPARGC1A cd12623
RNA recognition motif (RRM) found in peroxisome proliferator-activated receptor gamma ...
 656-700 1.46e-03

RNA recognition motif (RRM) found in peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1alpha, or PPARGC-1-alpha) and similar proteins; This subgroup corresponds to the RRM of PGC-1alpha, also termed PPARGC-1-alpha, or ligand effect modulator 6, a member of a family of transcription coactivators that plays a central role in the regulation of cellular energy metabolism. As an inducible transcription coactivator, PGC-1alpha can interact with a broad range of transcription factors involved in a wide variety of biological responses, such as adaptive thermogenesis, skeletal muscle fiber type switching, glucose/fatty acid metabolism, and heart development. PGC-1alpha stimulates mitochondrial biogenesis and promotes oxidative metabolism. It participates in the regulation of both carbohydrate and lipid metabolism and plays a role in disorders such as obesity, diabetes, and cardiomyopathy. PGC-1alpha is a multi-domain protein containing an N-terminal activation domain region, a central region involved in the interaction with at least a nuclear receptor, and a C-terminal domain region. The N-terminal domain region consists of three leucine-rich motifs (L1, NR box 2 and 3), among which the two last are required for interaction with nuclear receptors, potential nuclear localization signals (NLS), and a proline-rich region overlapping a putative repression domain. The C-terminus of PGC-1alpha is composed of two arginine/serine-rich regions (SR domains), a putative dimerization domain, and an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). PGC-1alpha could interact favorably with single-stranded RNA.


Pssm-ID: 410034 [Multi-domain]  Cd Length: 91  Bit Score: 41.03  E-value: 1.46e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24580581  656 RTLFIGNLEKDITAGELRSHFEAFGEIIE--IDIKKQGlNAYAFCQY 700
Cdd:cd12623    3 RVIYVGKIRPDITRTELKRRFEVFGEIEEctVNLRDDG-DSYGFITY 48
RRM2_CoAA cd12609
RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator ...
 658-723 1.60e-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: 40.22  E-value: 1.60e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQglnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRI 723
Cdd:cd12609    3 IFVGNVSATCTSDELRGLFEEFGRVVECDKVKD----YAFVHMEREEEALAAIEALNGKEVKGRRI 64
RRM4_I_PABPs cd12381
RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...
 737-806 1.60e-03

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: 40.33  E-value: 1.60e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24580581  737 WIDGVDEKVSESFLQSQFTRFGAVT--KVSID---RNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDFASR 806
Cdd:cd12381    5 YVKNLDDTIDDEKLREEFSPFGTITsaKVMTDeggRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALAQR 79
CAF-1_p150 pfam11600
Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide ...
 1943-2087 1.62e-03

Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesized and acetylated histones H3/H4 into chromatin during DNA replication and repair. CAF-1_p150 includes the HP1 interaction site, the PEST, KER and ED interacting sites. CAF-1_p150 interacts directly with newly synthesized and acetylated histones through the acidic KER and ED domains. The PEST domain is associated with proteins that undergo rapid proteolysis.


Pssm-ID: 402959 [Multi-domain]  Cd Length: 164  Bit Score: 42.75  E-value: 1.62e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1943 EREEKDRKAQQEERekedrkakeeekereREKKAQEDREKKEREERELREKEQRDKEQKEKEIREKDLREKEQRERDNRE 2022
Cdd:pfam11600    9 SQEEKEKQRLEKDK---------------ERLRRQLKLEAEKEEKERLKEEAKAEKERAKEEARRKKEEEKELKEKERRE 73

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24580581   2023 KELRDKDLREKEMREKEQREKELHREKDQREREHREKEQSRRAMDVEQEGRGGRMRELSSYQKSK 2087
Cdd:pfam11600   74 KKEKDEKEKAEKLRLKEEKRKEKQEALEAKLEEKRKKEEEKRLKEEEKRIKAEKAEITRFLQKPK 138
RRM3_RAVER cd12390
RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
 656-728 1.68e-03

RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409824 [Multi-domain]  Cd Length: 91  Bit Score: 40.68  E-value: 1.68e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581  656 RTLFIGNLEKDIT-AGELRSHFEAFGEII--EIDIKKQGLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFG 728
Cdd:cd12390    3 KCLFVDRLPKDFRdGSELRKLFSQVGKPTfcQLAMGNGVPRGFAFVEFASAEDAEEAQQLLNGHDLQGSPIRVSFG 78
RRM_YRA2 cd12295
RNA recognition motif in yeast RNA annealing protein YRA2 (Yra2p) and similar proteins; This ...
 556-631 1.96e-03

RNA recognition motif in yeast RNA annealing protein YRA2 (Yra2p) and similar proteins; This subfamily corresponds to the RRM of Yra2p, a nonessential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA2 gene. It may share some overlapping functions with Yra1p, and is able to complement an YRA1 deletion when overexpressed in yeast. Yra2p belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. It is a major component of endogenous Yra1p complexes. It interacts with Yra1p and functions as a negative regulator of Yra1p. Yra2p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409736 [Multi-domain]  Cd Length: 74  Bit Score: 40.12  E-value: 1.96e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581  556 IRVRNLPARSSDTSLKDGLfheyKKHGKVTWVKVVGQNSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEVEPYQ 631
Cdd:cd12295    3 LRITNIPLDVSDYTIEDMI----KEFGEPEYINFYDHKDSRSAIFEFEDPEILEKAVEKYNGKELHGAKIEVEIFE 74
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
 558-627 2.09e-03

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: 40.23  E-value: 2.09e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24580581  558 VRNLPARSSDTSLKDgLFheyKKHGKVTWVKVVGQ---NSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEV 627
Cdd:cd12380    6 VKNFGEDVDDDELKE-LF---EKYGKITSAKVMKDdsgKSKGFGFVNFENHEAAQKAVEELNGKELNGKKLYV 74
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
 656-724 2.25e-03

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: 40.01  E-value: 2.25e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24580581  656 RTLFIGNLEKDITAGELRSHFEAFGEIIEIDI------KKQGLnayAFCQYSDIVSVVKAMRKMDGEHLGSNRIK 724
Cdd:cd12392    3 NKLFVKGLPFSCTKEELEELFKQHGTVKDVRLvtyrngKPKGL---AYVEYENEADASQAVLKTDGTEIKDHTIS 74
PRK12704 PRK12704
phosphodiesterase; Provisional
 1999-2099 2.32e-03

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 44.38  E-value: 2.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  1999 EQKEKEIREKDLREKEQRERDN----REKELRDKDLR-EKEMREKEQREKELhrEKDQREREHREKEQSRRAMDVEqegr 2073
Cdd:PRK12704   61 EAKEEIHKLRNEFEKELRERRNelqkLEKRLLQKEENlDRKLELLEKREEEL--EKKEKELEQKQQELEKKEEELE---- 134

                          90       100
                  ....*....|....*....|....*.
gi 24580581  2074 ggrmrELSSYQKSKMDiagEASSLTA 2099
Cdd:PRK12704  135 -----ELIEEQLQELE---RISGLTA 152
DUF4200 pfam13863
Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil ...
 1999-2061 2.38e-03

Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil domain of unknwon function.


Pssm-ID: 464003 [Multi-domain]  Cd Length: 119  Bit Score: 41.01  E-value: 2.38e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1999 EQKEKEI---------REKDLREKEQ--RE---------RDNREKELRDKDLREKEMREKEQREKELHREKDQREREHRE 2058
Cdd:pfam13863   16 DAKREEIerleellkqREEELEKKEQelKEdlikfdkflKENDAKRRRALKKAEEETKLKKEKEKEIKKLTAQIEELKSE 95


                   ...
gi 24580581   2059 KEQ 2061
Cdd:pfam13863   96 ISK 98
rRNA_processing pfam08524
rRNA processing; This is a family of proteins that are involved in rRNA processing. In a ...
 1997-2071 2.42e-03

rRNA processing; This is a family of proteins that are involved in rRNA processing. In a localization study they were found to localize to the nucleus and nucleolus. The family also includes other metazoa members from plants to mammals where the protein has been named BR22 and is associated with TTF-1, thyroid transcription factor 1. In the lungs, the family binds TTF-1 to form a complex which influences the expression of the key lung surfactant protein-B (SP-B) and -C (SP-C), the small hydrophobic surfactant proteins that maintain surface tension in alveoli.


Pssm-ID: 400708 [Multi-domain]  Cd Length: 142  Bit Score: 41.52  E-value: 2.42e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1997 DKEQKEKEIrEKDLREKEqRERDNREKELRD-----------------------KDLREKEMREKEQREKELHREKdQRE 2053
Cdd:pfam08524    8 DKEYKSKEI-QKSLTRKA-RLRKEYFKALKKegyevpekangsngeeentskslKEARELQGKTKFDERKEIKKER-KEE 84

                           90
                   ....*....|....*...
gi 24580581   2054 REHREKEQSRRAMDVEQE 2071
Cdd:pfam08524   85 KRERKLEARQKKLERIKA 102
RRM2_FCA cd12637
RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar ...
 658-717 2.52e-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: 40.06  E-value: 2.52e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKK----QGLNAYAFCQYSDIVSVVKAMRKMDGEH 717
Cdd:cd12637    2 LFVGSLPKTATEQEVRDLFEAYGEVEEVYLMKdpvtQQGTGCAFVKFAYKEEALAAIRSLNGTV 65
RRM1_TIA1_like cd12352
RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and ...
 658-724 2.63e-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: 39.70  E-value: 2.63e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEI--IEIDIKKQGLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIK 724
Cdd:cd12352    1 LYVGNLDRQVTEDLILQLFSQIGPCksCKMITEHGGNDPYCFVEFYEHNHAAAALQAMNGRKILGKEVK 69
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
 745-804 2.66e-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: 39.85  E-value: 2.66e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24580581  745 VSESFLQSQFTRFGAVTKVSIDRN-----RQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDFA 804
Cdd:cd12565   12 VTEKRLKEHFSKKGEITDVKVMRTkdgksRRFGFIGFKSEEEAQKAVKYFNKTFIDTSKISVEFA 76
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 1938-2071 2.85e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 44.16  E-value: 2.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 1938 LRKQVEREEKDRKAQQEERekedrkakeeekererekkaqedrekkereerELREKEQRDKEQKEKEIREKDLREKEQRE 2017
Cdd:COG1196  293 LLAELARLEQDIARLEERR--------------------------------RELEERLEELEEELAELEEELEELEEELE 340

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 24580581 2018 RDNREKELRDKDLREKEMREKEQREKELHREKDQREREHREKEQSRRAMDVEQE 2071
Cdd:COG1196  341 ELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRA 394
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
 658-729 2.96e-03

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: 39.73  E-value: 2.96e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDI-------KKQGlnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFGK 729
Cdd:cd12397    1 LFVGNLSFETTEEDLRKHFAPAGKIRKVRMatfedsgKCKG---FAFVDFKEIESATNAVKGPINHSLNGRDLRVEYGE 76
RRM_ist3_like cd12411
RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ...
 648-724 3.09e-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: 3.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  648 DEYhpKSTRTLFIGNLEKDITAGELRSHFEAFGEIIEIDI---KKQGLN-AYAFCQYSDIVSVVKAMRKMDGEHLGSNRI 723
Cdd:cd12411    4 DEY--KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLvrdKKTGKSkGFAFLAYEDQRSTILAVDNLNGIKLLGRTI 81


                 .
gi 24580581  724 K 724
Cdd:cd12411   82 R 82
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
 738-804 3.21e-03

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: 39.44  E-value: 3.21e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  738 IDGVDEKVSESFLQSQ----FTRFGAVTKVSIDRNRQL---ALVLYDQVQNAQAAVKDMRGTILRRKKLQVDFA 804
Cdd:cd12246    4 INNLNEKIKKDELKRSlyalFSQFGPVLDIVASKSLKMrgqAFVVFKDVESATNALRALQGFPFYGKPMRIQYA 77
RRM1_SF2_plant_like cd12599
RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar ...
 657-725 3.29e-03

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: 39.35  E-value: 3.29e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24580581  657 TLFIGNLEKDITAGELRSHFEAFGEIIEIDIkKQGLN--AYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKL 725
Cdd:cd12599    1 RVYVGNLPMDIREREVEDLFSKYGPVVSIDL-KIPPRppAYAFVEFEDARDAEDAIRGRDGYDFDGHRLRV 70
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 1997-2073 3.48e-03

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: 43.75  E-value: 3.48e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1997 DKEQKEKEIREKDL-REKE-QRERDNREKELRDKD-LREKEMREKEQREKELHREkdqREREHREKEQSRRAMDVEQEGR 2073
Cdd:TIGR01622   18 DRDRRRDKGRERSRdRSRDrERSRSRRRDRHRDRDyYRGRERRSRSRRPNRRYRP---REKRRRRGDSYRRRRDDRRSRR 94
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
 736-795 3.50e-03

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: 39.23  E-value: 3.50e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  736 VWIDGVDEKVSESFLQSQFTRFGAVTKVSIDRNRQLALVLYDQVQNAQAAVKDMRGTILR 795
Cdd:cd12346    4 VFVGGLDPNVTEEDLRVLFGPFGEIVYVKIPPGKGCGFVQFVNRASAEAAIQKLQGTPIG 63
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
 736-806 3.54e-03

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: 39.15  E-value: 3.54e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24580581  736 VWIDGVDEKVSESFLQSQFTRFGAVTKVSIDRNRQ-LALVLYDQVQNAQAAVKDMRGTILRRKKLQVDFASR 806
Cdd:cd12373    2 VYVGNLGPRVTKRELEDAFEKYGPLRNVWVARNPPgFAFVEFEDPRDAEDAVRALDGRRICGSRVRVELSRG 73
RRM1_SRSF9 cd12598
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 9 ...
 658-727 3.61e-03

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: 39.40  E-value: 3.61e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIK-KQGLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGF 727
Cdd:cd12598    2 IYVGNLPSDVREKDLEDLFYKYGRIRDIELKnRRGLVPFAFVRFEDPRDAEDAVFGRNGYDFGQCRLRVEF 72
RRM_SF3B14 cd12241
RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar ...
 654-715 3.61e-03

RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins; This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409687 [Multi-domain]  Cd Length: 77  Bit Score: 39.14  E-value: 3.61e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24580581  654 STRTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQ-GLNAYAFCQYSDIVSVVKAMRKMDG 715
Cdd:cd12241    1 VNRILYVRNLPYKISSEELYDLFGKYGAIRQIRIGNTkETRGTAFVVYEDIFDAKNACDHLSG 63
RRM2_PUB1 cd12619
RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated ...
 658-724 3.67e-03

RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM2 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: 410031 [Multi-domain]  Cd Length: 80  Bit Score: 39.40  E-value: 3.67e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEI----DIKKQGLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIK 724
Cdd:cd12619    4 IFVGDLSPEVTDAALFNAFSDFPSCSDArvmwDQKTGRSRGYGFVSFRSQQDAQNAINSMNGKWLGSRPIR 74
PTZ00121 PTZ00121
MAEBL; Provisional
 1912-2109 3.73e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 43.98  E-value: 3.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  1912 DTADKAEKNQRHEKEKKERQEKREKDLRK--QVEREEKDR----KAQQEEREKEDRKAKEEEKEREREKKAQEDREKKER 1985
Cdd:PTZ00121 1537 DEAKKAEEKKKADELKKAEELKKAEEKKKaeEAKKAEEDKnmalRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAE 1616

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  1986 EERELREKEQRDKEQKEKEIREKDLREKEQRERDNREKELRDKDLREKEMREKEQREKELHREKDQREREHREKEQSRRA 2065
Cdd:PTZ00121 1617 EAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKK 1696

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 24580581  2066 mDVEQEGRGGRMRELSSYQKSKMDIAGEASSLTAIDCQHNKENA 2109
Cdd:PTZ00121 1697 -EAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEA 1739
petO cd22950
Cytochrome b6-f complex subunit petO; Chloroplastic cytochrome b6-f complex subunit petO (or ...
 4587-4709 3.78e-03

Cytochrome b6-f complex subunit petO; Chloroplastic cytochrome b6-f complex subunit petO (or PETO), also called cytochrome b6-f complex subunit V (suV) or cytochrome b6-f-associated phosphoprotein, is a novel cytochrome b6-f subunit specific in green algae that is predicted by sequence analysis and biochemical characterization to have a one transmembrane alpha-helix topology with two large hydrophilic domains extending on the stromal and lumenal side of the thylakoid membranes, with a lumenal location of the N-terminus. It is reversibly phosphorylated upon state transition, and may have a possible role in signal transduction during redox-controlled short term and long term adaptation of the eukaryotic photosynthetic apparatus. PetO has been shown to contribute to the cyclic electron flow (CEF) around photosystem I (PSI) and cytochrome b6-f that generates ATP.


Pssm-ID: 438570  Cd Length: 165  Bit Score: 41.39  E-value: 3.78e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581 4587 IEEVTASNATVAASHL--APPEGAGVESHVPQLDAkevepvsvVTPISTPAPVSVAAPVTVPVPAMVPVKPTmPQHPKKK 4664
Cdd:cd22950   12 AEEQAQAAAAAAAAALltASPANAGVVLQQPELKK--------VFQDDSPAAAAPKREFKGPPALPAPTAAA-PAAAKEK 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 24580581 4665 AiaAAEIESyqainssiPSGGLPMHQTAAPATQKITGGVADAVSK 4709
Cdd:cd22950   83 K--AEVVES--------SSGGLDPRSVALPAALVFVIGGAFAASK 117
RRM1_SRSF5 cd12595
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 ...
 658-725 4.00e-03

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: 39.16  E-value: 4.00e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKkqglNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKL 725
Cdd:cd12595    2 VFIGRLNPAAREKDVERFFKGYGRIRDIDLK----RGFGFVEFEDPRDADDAVYELDGKELCNERVTI 65
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
 750-801 4.26e-03

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: 39.14  E-value: 4.26e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 24580581  750 LQSQFTRFGAV--TKVSIDRNRQL----ALVLYDQVQNAQAAVKDMRGTILRRKKLQV 801
Cdd:cd12362   15 LYQLFAPFGNVvsAKVFVDKNTGRskgfGFVSYDNPLSAQAAIKAMNGFQVGGKRLKV 72
RRM1_RBM19 cd12564
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
 658-723 4.31e-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: 4.31e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIK--KQG-LNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRI 723
Cdd:cd12564    3 LIVKNLPSSITEDRLRKLFSAFGTITDVQLKytKDGkFRRFGFVGFKSEEEAQKALKHFNNSFIDTSRI 71
RRM1_RBM15B cd12554
RNA recognition motif 1 (RRM1) found in putative RNA binding motif protein 15B (RBM15B) from ...
 558-629 4.37e-03

RNA recognition motif 1 (RRM1) found in putative RNA binding motif protein 15B (RBM15B) from vertebrate; This subfamily corresponds to the RRM1 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: 409970 [Multi-domain]  Cd Length: 80  Bit Score: 39.42  E-value: 4.37e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  558 VRNLPARSSDTSLKDGLFHEYKKHGKVTwVKvVGQNSE--RYALVCFKKPDDVEKALEVSHDKHFFGCKIEVEP 629
Cdd:cd12554    7 VSNLGSQLPDELLEDGLFHEFKKFGEVS-VK-LSHTPElgRVAYVNFRHPEDAKEARHAKGRLVLYDRPLKVEP 78
RRM2_hnRNPA_like cd12328
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
 658-709 4.49e-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: 38.79  E-value: 4.49e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDI-------KKQGlnaYAFCQYSDIVSVVKA 709
Cdd:cd12328    2 LFVGGLKEDVEEEDLREYFSQFGKVESVEIvtdketgKKRG---FAFVTFDDHDSVDKI 57
RRM_RBM42 cd12383
RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This ...
 658-725 4.50e-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: 39.18  E-value: 4.50e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDI-------KKQGlnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKL 725
Cdd:cd12383    9 IFCGDLGNEVTDEVLARAFSKYPSFQKAKVirdkrtgKSKG---YGFVSFKDPNDYLKALREMNGKYVGNRPIKL 80
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 558-628 4.54e-03

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: 39.11  E-value: 4.54e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581  558 VRNLPARSSDTSLKDgLFHEykkHGKV--TWVkVVGQNSER---YALVCFKKPDDVEKALEVSHDKHFFGCKIEVE 628
Cdd:cd12413    4 VRNLPYDTTDEQLEE-LFSD---VGPVkrCFV-VKDKGKDKcrgFGYVTFALAEDAQRALEEVKGKKFGGRKIKVE 74
PTZ00121 PTZ00121
MAEBL; Provisional
 1909-2219 4.71e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 43.59  E-value: 4.71e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  1909 EADDTADKAEKNQRHEKEKKERQEKREKDLRK--QVEREEKDRKAQQEErekedRKAKEEEKEREREKKAQEDREKKERE 1986
Cdd:PTZ00121 1617 EAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKaeELKKAEEENKIKAAE-----EAKKAEEDKKKAEEAKKAEEDEKKAA 1691

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  1987 ERELREKEQRDKEQKEKEIREKDLREKEQRERDNREKELRDKDLREKEMREKEQREKELHREKDQREREHREKEQSRRAM 2066
Cdd:PTZ00121 1692 EALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAE 1771

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  2067 DVEQEGRGGRMRELssyqKSKMDIAGEASSLTAIDCQHNKENAMDTIAQGTPGASPSTP-----------SDNTPKERSR 2135
Cdd:PTZ00121 1772 EIRKEKEAVIEEEL----DEEDEKRRMEVDKKIKDIFDNFANIIEGGKEGNLVINDSKEmedsaikevadSKNMQLEEAD 1847

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  2136 KLSRNspvRLHKRRLSSQESNHSAGGGGSCGGSSHQIHHEDYVKRIRMENSQNISVHSSNQRL----NDRRDSKEHKSSS 2211
Cdd:PTZ00121 1848 AFEKH---KFNKNNENGEDGNKEADFNKEKDLKEDDEEEIEEADEIEKIDKDDIEREIPNNNMagknNDIIDDKLDKDEY 1924


                  ....*...
gi 24580581  2212 FKEDKNSS 2219
Cdd:PTZ00121 1925 IKRDAEET 1932
RRM_PPARGC1B cd12356
RNA recognition motif (RRM) found in peroxisome proliferator-activated receptor gamma ...
 656-702 4.98e-03

RNA recognition motif (RRM) found in peroxisome proliferator-activated receptor gamma coactivator 1-beta (PGC-1-beta) and similar proteins; This subfamily corresponds to the RRM of PGC-1beta, also termed PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or PGC-1-related estrogen receptor alpha coactivator, which is one of the members of PGC-1 transcriptional coactivators family, including PGC-1alpha and PGC-1-related coactivator (PRC). PGC-1beta plays a nonredundant role in controlling mitochondrial oxidative energy metabolism and affects both, insulin sensitivity and mitochondrial biogenesis, and functions in a number of oxidative tissues. It is involved in maintaining baseline mitochondrial function and cardiac contractile function following pressure overload hypertrophy by preserving glucose metabolism and preventing oxidative stress. PGC-1beta induces hypertriglyceridemia in response to dietary fats through activating hepatic lipogenesis and lipoprotein secretion. It can stimulate apolipoprotein C3 (APOC3) expression, further mediating hypolipidemic effect of nicotinic acid. PGC-1beta also drives nuclear respiratory factor 1 (NRF-1) target gene expression and NRF-1 and estrogen related receptor alpha (ERRalpha)-dependent mitochondrial biogenesis. The modulation of the expression of PGC-1beta can trigger ERRalpha-induced adipogenesis. PGC-1beta is also a potent regulator inducing angiogenesis in skeletal muscle. The transcriptional activity of PGC-1beta can be increased through binding to host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. PGC-1beta is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, two glutamic/aspartic acid-rich acidic domains, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha, PGC-1beta lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing.


Pssm-ID: 409792 [Multi-domain]  Cd Length: 97  Bit Score: 39.56  E-value: 4.98e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 24580581  656 RTLFIGNLEKDITAGELRSHFEAFGEIIEIDI--KKQGLNAYAFCQYSD 702
Cdd:cd12356    8 RVVYIRNLSSSMSSNELKRRFEVFGEITECCVlsRSNRGEKYGFITYRD 56
RRM_TRA2B cd12641
RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and ...
 732-805 5.13e-03

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: 39.22  E-value: 5.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  732 PTNCVWIDGVDEKVSESFLQSQFTRFGAVTKVSI------DRNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDFAS 805
Cdd:cd12641    6 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIvydqqsRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSI 85
DUF4670 pfam15709
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ...
 1997-2093 5.35e-03

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.


Pssm-ID: 464815 [Multi-domain]  Cd Length: 522  Bit Score: 43.02  E-value: 5.35e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1997 DKEQKEKEIREKDLREKEQRERdnREKELRDKDLREKEMREKEQREKELHREKDQREREHREKEQSRRAMDVEQEGRGGR 2076
Cdd:pfam15709  381 EQQRRFEEIRLRKQRLEEERQR--QEEEERKQRLQLQAAQERARQQQEEFRRKLQELQRKKQQEEAERAEAEKQRQKELE 458

                           90
                   ....*....|....*..
gi 24580581   2077 MReLSSYQKSKMDIAGE 2093
Cdd:pfam15709  459 MQ-LAEEQKRLMEMAEE 474
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
 745-804 5.63e-03

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: 38.69  E-value: 5.63e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581  745 VSESFLQSQFTRFGAVTKVSI--D----RNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDFA 804
Cdd:cd21608   11 TTEDDLRDLFSEFGEVESAKVitDretgRSRGFGFVTFSTAEAAEAAIDALNGKELDGRSIVVNEA 76
RRM1_SXL cd12649
RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
 657-730 5.77e-03

RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. 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 also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 241093 [Multi-domain]  Cd Length: 81  Bit Score: 38.92  E-value: 5.77e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24580581  657 TLFIGNLEKDITAGELRSHFEAFGEIIEIDI---KKQGLN-AYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFGKS 730
Cdd:cd12649    2 NLIVNYLPQDLTDREFRALFRAIGPVNTCKIvrdKKTGYSyGFGFVDFTSEEDAQRAIKTLNGLQLQNKRLKVAYARP 79
RRM1_p54nrb_like cd12332
RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
 745-803 5.91e-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: 38.43  E-value: 5.91e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 24580581  745 VSESFLQSQFTRFGAVTKVSIDRNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDF 803
Cdd:cd12332   13 ITEEEFKELFQKYGEVSEVFLNKGKGFGFIRLDTRANAEAAKAELDGTPRKGRQLRVRF 71
DUF4659 pfam15558
Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins ...
 1998-2110 6.91e-03

Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins in this family are typically between 427 and 674 amino acids in length. There are two completely conserved residues (D and I) that may be functionally important.


Pssm-ID: 464768 [Multi-domain]  Cd Length: 374  Bit Score: 42.33  E-value: 6.91e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1998 KEQKEKEIREKDLREKEQRERDNREKELRDKDlreKEMREKEQREKE-LHREKDQREREHREKEQSRRAMDVEQEGRGGR 2076
Cdd:pfam15558  190 QAKAEELLRRLSLEQSLQRSQENYEQLVEERH---RELREKAQKEEEqFQRAKWRAEEKEEERQEHKEALAELADRKIQQ 266

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 24580581   2077 MRELSSYQ-KSKMDIAGEASSLTAiDCQH-NKENAM 2110
Cdd:pfam15558  267 ARQVAHKTvQDKAQRARELNLERE-KNHHiLKLKVE 301
RRM2_I_PABPs cd12379
RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This ...
 658-715 6.93e-03

RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM2 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 a 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. 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: 409813 [Multi-domain]  Cd Length: 77  Bit Score: 38.71  E-value: 6.93e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDI---KKQGLNAYAFCQYSDIVSVVKAMRKMDG 715
Cdd:cd12379    5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVatdENGGSKGYGFVHFETEEAAERAIEKVNG 65
RRM_TRA2 cd12363
RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and ...
 733-804 7.06e-03

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: 38.75  E-value: 7.06e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24580581  733 TNCVWIDGVDEKVSESFLQSQFTRFGAVTKVSI------DRNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDFA 804
Cdd:cd12363    1 SRCLGVFGLSLYTTERDLREVFSRYGPIEKVQVvydqqtGRSRGFGFVYFESVEDAKEAKERLNGQEIDGRRIRVDYS 78
Nop53 pfam07767
Nop53 (60S ribosomal biogenesis); This nucleolar family of proteins are involved in 60S ...
 2002-2070 7.25e-03

Nop53 (60S ribosomal biogenesis); This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins.


Pssm-ID: 462259 [Multi-domain]  Cd Length: 353  Bit Score: 42.28  E-value: 7.25e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24580581   2002 EKEIREKDLREKEQRERDNREKELRDKDLREKEMREKEQREKELhREKDQREREHREKEQSRRAMDVEQ 2070
Cdd:pfam07767  206 EAEKKRLKEEEKLERVLEKIAESAATAEAREEKRKTKAQRNKEK-RRKEEEREAKEEKALKKKLAQLER 273
PRK00247 PRK00247
putative inner membrane protein translocase component YidC; Validated
 1997-2136 7.46e-03

putative inner membrane protein translocase component YidC; Validated


Pssm-ID: 178945 [Multi-domain]  Cd Length: 429  Bit Score: 42.53  E-value: 7.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  1997 DKEQKEKEIREKDLREKEQRERDNREKELRDK------------DLREKEMREKEQREKELHREKDQREREHREKEQSRR 2064
Cdd:PRK00247  280 TDEFKEHHAEQRAQYREKQKEKKAFLWTLRRNrlrmiitpwrapELHAENAEIKKTRTAEKNEAKARKKEIAQKRRAAER 359

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24580581  2065 AMDVEQ-EGRGGRMRELSSYQKSKmdiagEASSLTAIDCQHNKENAMDtiAQGTPGASPSTPSDNTPKERSRK 2136
Cdd:PRK00247  360 EINREArQERAAAMARARARRAAV-----KAKKKGLIDASPNEDTPSE--NEESKGSPPQVEATTTAEPNREP 425
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
 658-789 7.58e-03

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.


Pssm-ID: 130706 [Multi-domain]  Cd Length: 612  Bit Score: 42.75  E-value: 7.58e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581    658 LFIGNLEKDITAGELRSHFEAFGEIIEIDIK----KQGLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFGKSMPT 733
Cdd:TIGR01645  110 VYVGSISFELREDTIRRAFDPFGPIKSINMSwdpaTGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQ 189

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580581    734 ---------------NCVWIDGVDEKVSESFLQSQFTRFGAVTKVSIDR------NRQLALVLYDQVQNAQAAVKDM 789
Cdd:TIGR01645  190 aqpiidmvqeeakkfNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARaptgrgHKGYGFIEYNNLQSQSEAIASM 266
RRM1_U1A cd12477
RNA recognition motif 1 (RRM1) found in vertebrate U1 small nuclear ribonucleoprotein A (U1A); ...
 732-807 8.11e-03

RNA recognition motif 1 (RRM1) found in vertebrate U1 small nuclear ribonucleoprotein A (U1A); This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), 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 and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import.


Pssm-ID: 409906 [Multi-domain]  Cd Length: 89  Bit Score: 38.81  E-value: 8.11e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581  732 PTNCVWIDGVDEKVSESFLQSQ----FTRFGAVTKVSIDRNRQL---ALVLYDQVQNAQAAVKDMRGTILRRKKLQVDFA 804
Cdd:cd12477    2 PNHTIYINNLNEKIKKDELKKSlhaiFSRFGQILDILVSRSLKMrgqAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 81


                 ...
gi 24580581  805 SRE 807
Cdd:cd12477   82 KTD 84
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 658-715 8.43e-03

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: 38.30  E-value: 8.43e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  658 LFIGNLEKDITAGELRSHFEAFGEIIEIDI------KKQGlnaYAFCQYSDIVSVVKAMRKMDG 715
Cdd:cd12414    2 LIVRNLPFKCTEDDLKKLFSKFGKVLEVTIpkkpdgKLRG---FAFVQFTNVADAAKAIKGMNG 62
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
 736-805 8.67e-03

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: 38.43  E-value: 8.67e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24580581  736 VWIDGVDEKVSESFLQSQFTRFGAVTKVSI---------DRNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDFAS 805
Cdd:cd12355    2 LWIGNLDPRLTEYHLLKLLSKYGKIKKFDFlfhktgplkGQPRGYCFVTFETKEEAEKAIECLNGKLALGKKLVVRWAH 80
PRK12704 PRK12704
phosphodiesterase; Provisional
 1998-2065 8.71e-03

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 42.46  E-value: 8.71e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580581  1998 KEQKEKEIREK--DLREKEQRERDnREKELRDK----DLREKEMREKEQREKELHREKDQREREHREKEQSRRA 2065
Cdd:PRK12704   70 RNEFEKELRERrnELQKLEKRLLQ-KEENLDRKlellEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQ 142
RRM4_RBM45 cd12369
RNA recognition motif 4 (RRM4) found in RNA-binding protein 45 (RBM45) and similar proteins; ...
 746-801 8.88e-03

RNA recognition motif 4 (RRM4) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM4 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: 409804 [Multi-domain]  Cd Length: 68  Bit Score: 38.04  E-value: 8.88e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24580581  746 SESFLQSQFTRFGAVTKVSIDRNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQV 801
Cdd:cd12369   12 PLDILEDVFCRFGNLIDVYLVPGKNVGYAKYADRESAEEAITTLHGKEVNGVKLKV 67
RRM1_SNF cd12476
RNA recognition motif 1 (RRM1) found in Drosophila melanogaster sex determination protein SNF ...
 653-715 8.99e-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: 38.36  E-value: 8.99e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24580581  653 KSTRTLFIGNLEKDITAGELRSH----FEAFGEIIEI-DIKKQGLNAYAFCQYSDIVSVVKAMRKMDG 715
Cdd:cd12476    4 RPNQTIYINNLNEKVKKEELKKSlyaiFSQFGQILDIvALKTLKMRGQAFVIFKDISSATNALRSMQG 71
DUF4659 pfam15558
Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins ...
 1999-2071 9.35e-03

Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins in this family are typically between 427 and 674 amino acids in length. There are two completely conserved residues (D and I) that may be functionally important.


Pssm-ID: 464768 [Multi-domain]  Cd Length: 374  Bit Score: 41.95  E-value: 9.35e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580581   1999 EQKEKEIREKDLREKEQ----RERDNREKELRDKDLR------EKEMREKEQREKELHREKDQRERE---HREKEQSRRA 2065
Cdd:pfam15558  218 EERHRELREKAQKEEEQfqraKWRAEEKEEERQEHKEalaelaDRKIQQARQVAHKTVQDKAQRARElnlEREKNHHILK 297


                   ....*.
gi 24580581   2066 MDVEQE 2071
Cdd:pfam15558  298 LKVEKE 303
 
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.
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