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Conserved domains on  [gi|564399098|ref|XP_006256949|]
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U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 isoform X1 [Rattus norvegicus]

Protein Classification

U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2( domain architecture ID 10458020)

U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 is a pre-mRNA-binding protein required for splicing of both U2- and U12-type introns

Gene Symbol:  ZRSR2
PubMed:  22278943|12665246

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM_U2AFBPL cd12540
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor 35 ...
199-303 6.88e-65

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL) and similar proteins; This subgroup corresponds to the RRM of U2AFBPL, a human homolog of the imprinted mouse gene U2afbp-rs, which encodes a U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL), also termed CCCH type zinc finger, RNA-binding motif and serine/arginine rich protein 1 (U2AF1RS1), or U2 small nuclear RNA auxiliary factor 1-like 1 (U2AF1L1). Although the biological role of U2AFBPL remains unclear, it shows high sequence homology to splicing factor U2AF 35 kDa subunit (U2AF35 or U2AF1) that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. Like U2AF35, U2AFBPL contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain.


:

Pssm-ID: 409956 [Multi-domain]  Cd Length: 105  Bit Score: 206.35  E-value: 6.88e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564399098 199 TLLIKSMFTTFGMEQCRRDDYDPDSSLEYSEEETYQQFLDFYYDVLPEFKSVGKVIQFKVSCNLEPHLRGNVYVQYQSEE 278
Cdd:cd12540    1 TLLIPNMFNTFGLEQCKRDDYDTDAGLEYSEEDLYSDFLEFYEDVLPEFKKFGKVVQFKVCCNSEPHLRGNVYVQYQSEE 80
                         90       100
                 ....*....|....*....|....*
gi 564399098 279 DCQAAFSVFNGRWYAGRQLQCEFCP 303
Cdd:cd12540   81 EALKAFTSFNGRWYAGKQLQCEFSP 105
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
167-191 9.71e-06

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


:

Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 42.18  E-value: 9.71e-06
                          10        20
                  ....*....|....*....|....*
gi 564399098  167 KDRANCPFYSKTGACRFGDRCSRKH 191
Cdd:pfam00642   1 YKTELCRFFLRTGYCKYGDRCKFAH 25
ZnF_C3H1 smart00356
zinc finger;
306-331 5.05e-03

zinc finger;


:

Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 34.53  E-value: 5.05e-03
                           10        20
                   ....*....|....*....|....*.
gi 564399098   306 RWKMAICGLFEVQQCPRGKHCNFLHV 331
Cdd:smart00356   1 KYKTELCKFFKRGYCPRGDRCKFAHP 26
 
Name Accession Description Interval E-value
RRM_U2AFBPL cd12540
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor 35 ...
199-303 6.88e-65

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL) and similar proteins; This subgroup corresponds to the RRM of U2AFBPL, a human homolog of the imprinted mouse gene U2afbp-rs, which encodes a U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL), also termed CCCH type zinc finger, RNA-binding motif and serine/arginine rich protein 1 (U2AF1RS1), or U2 small nuclear RNA auxiliary factor 1-like 1 (U2AF1L1). Although the biological role of U2AFBPL remains unclear, it shows high sequence homology to splicing factor U2AF 35 kDa subunit (U2AF35 or U2AF1) that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. Like U2AF35, U2AFBPL contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain.


Pssm-ID: 409956 [Multi-domain]  Cd Length: 105  Bit Score: 206.35  E-value: 6.88e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564399098 199 TLLIKSMFTTFGMEQCRRDDYDPDSSLEYSEEETYQQFLDFYYDVLPEFKSVGKVIQFKVSCNLEPHLRGNVYVQYQSEE 278
Cdd:cd12540    1 TLLIPNMFNTFGLEQCKRDDYDTDAGLEYSEEDLYSDFLEFYEDVLPEFKKFGKVVQFKVCCNSEPHLRGNVYVQYQSEE 80
                         90       100
                 ....*....|....*....|....*
gi 564399098 279 DCQAAFSVFNGRWYAGRQLQCEFCP 303
Cdd:cd12540   81 EALKAFTSFNGRWYAGKQLQCEFSP 105
RRM_1 smart00361
RNA recognition motif;
229-300 4.60e-17

RNA recognition motif;


Pssm-ID: 214637 [Multi-domain]  Cd Length: 70  Bit Score: 75.52  E-value: 4.60e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564399098   229 EEETYQQFLDFYYDVLPEFKSVGKVIQFKVSCnlEPHLRGNVYVQYQSEEDCQAAFSVFNGRWYAGRQLQCE 300
Cdd:smart00361   1 KDEDFERELKEEEEYFGEVGKINKIYIDDVGY--ENHKRGNVYITFERSEDAARAIVDLNGRYFDGRLVKAE 70
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
167-191 9.71e-06

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 42.18  E-value: 9.71e-06
                          10        20
                  ....*....|....*....|....*
gi 564399098  167 KDRANCPFYSKTGACRFGDRCSRKH 191
Cdd:pfam00642   1 YKTELCRFFLRTGYCKYGDRCKFAH 25
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
228-309 7.82e-05

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


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 45.30  E-value: 7.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564399098  228 SEEETYQQFLDFYYDVLPEFKSVGKVIQFKVscnLEPHLRGNVYVQYQSEEDCQAAFSVFNGRWYAGRQLQCEFCPVTRW 307
Cdd:TIGR01622 411 ATEEEPNWDKEIEDDVREECSKYGGVVHIYV---DDKNSAGDIYLKFDSVQAAEAAIKALNGRYFGGKMITAAFVVDAVY 487

                  ..
gi 564399098  308 KM 309
Cdd:TIGR01622 488 SK 489
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
242-297 5.43e-04

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: 38.37  E-value: 5.43e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 564399098  242 DVLPEFKSVGKVIQFKVSCNLEPHLRGNVYVQYQSEEDCQAAFSVFNGRWYAGRQL 297
Cdd:pfam00076  14 DLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69
ZnF_C3H1 smart00356
zinc finger;
306-331 5.05e-03

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 34.53  E-value: 5.05e-03
                           10        20
                   ....*....|....*....|....*.
gi 564399098   306 RWKMAICGLFEVQQCPRGKHCNFLHV 331
Cdd:smart00356   1 KYKTELCKFFKRGYCPRGDRCKFAHP 26
 
Name Accession Description Interval E-value
RRM_U2AFBPL cd12540
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor 35 ...
199-303 6.88e-65

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL) and similar proteins; This subgroup corresponds to the RRM of U2AFBPL, a human homolog of the imprinted mouse gene U2afbp-rs, which encodes a U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL), also termed CCCH type zinc finger, RNA-binding motif and serine/arginine rich protein 1 (U2AF1RS1), or U2 small nuclear RNA auxiliary factor 1-like 1 (U2AF1L1). Although the biological role of U2AFBPL remains unclear, it shows high sequence homology to splicing factor U2AF 35 kDa subunit (U2AF35 or U2AF1) that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. Like U2AF35, U2AFBPL contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain.


Pssm-ID: 409956 [Multi-domain]  Cd Length: 105  Bit Score: 206.35  E-value: 6.88e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564399098 199 TLLIKSMFTTFGMEQCRRDDYDPDSSLEYSEEETYQQFLDFYYDVLPEFKSVGKVIQFKVSCNLEPHLRGNVYVQYQSEE 278
Cdd:cd12540    1 TLLIPNMFNTFGLEQCKRDDYDTDAGLEYSEEDLYSDFLEFYEDVLPEFKKFGKVVQFKVCCNSEPHLRGNVYVQYQSEE 80
                         90       100
                 ....*....|....*....|....*
gi 564399098 279 DCQAAFSVFNGRWYAGRQLQCEFCP 303
Cdd:cd12540   81 EALKAFTSFNGRWYAGKQLQCEFSP 105
RRM_U2AF35_like cd12287
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ...
199-303 9.05e-39

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


Pssm-ID: 409729 [Multi-domain]  Cd Length: 101  Bit Score: 137.01  E-value: 9.05e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564399098 199 TLLIKSMFTTFGMEQCRrddyDPDSSLEYSEEETYQQFLDFYYDVLPEFKSVGKVIQFKVSCNLEPHLRGNVYVQYQSEE 278
Cdd:cd12287    1 TLLLKNMYPNPDNFISS----LDDGSLTLSEEEIQEHFDEFYEDVFLELSRFGEIEDLVVCSNLNDHLLGNVYVKFESEE 76
                         90       100
                 ....*....|....*....|....*
gi 564399098 279 DCQAAFSVFNGRWYAGRQLQCEFCP 303
Cdd:cd12287   77 DAEAALQALNGRYYAGRPLYPELSP 101
RRM_U2AF35B cd12539
RNA recognition motif (RRM) found in splicing factor U2AF 35 kDa subunit B (U2AF35B); This ...
198-303 8.25e-21

RNA recognition motif (RRM) found in splicing factor U2AF 35 kDa subunit B (U2AF35B); This subgroup corresponds to the RRM of U2AF35B, also termed zinc finger CCCH domain-containing protein 60 (C3H60), which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. Members in this family are mainly found in plant. They show high sequence homology to vertebrates U2AF35 that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. U2AF35B contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants.


Pssm-ID: 409955 [Multi-domain]  Cd Length: 102  Bit Score: 87.45  E-value: 8.25e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564399098 198 PTLLIKSMFTTFGMEQCRRDDYDPdsslEYSEEETYQQFLDFYYDVLPEFKSVGKVIQFKVSCNLEPHLRGNVYVQYQSE 277
Cdd:cd12539    1 PTILLSNMYQNPIMNAPLGAAQGI----PLDPRELQEHFEDFYEDVFEELSKFGEVEALNVCDNLGDHMVGNVYVKFRDE 76
                         90       100
                 ....*....|....*....|....*.
gi 564399098 278 EDCQAAFSVFNGRWYAGRQLQCEFCP 303
Cdd:cd12539   77 EHAAAALKALQGRFYAGRPIIVEFSP 102
RRM_1 smart00361
RNA recognition motif;
229-300 4.60e-17

RNA recognition motif;


Pssm-ID: 214637 [Multi-domain]  Cd Length: 70  Bit Score: 75.52  E-value: 4.60e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564399098   229 EEETYQQFLDFYYDVLPEFKSVGKVIQFKVSCnlEPHLRGNVYVQYQSEEDCQAAFSVFNGRWYAGRQLQCE 300
Cdd:smart00361   1 KDEDFERELKEEEEYFGEVGKINKIYIDDVGY--ENHKRGNVYITFERSEDAARAIVDLNGRYFDGRLVKAE 70
RRM_U2AF35 cd12538
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ...
197-303 1.31e-15

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35); This subgroup corresponds to the RRM of U2AF35, also termed U2AF1, which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF, U2AF65 (also termed U2AF2). U2AF35 contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich segment interrupted by glycines. U2AF35 binds both U2AF65 and the pre-mRNA through its RRM domain.


Pssm-ID: 409954 [Multi-domain]  Cd Length: 104  Bit Score: 72.78  E-value: 1.31e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564399098 197 SPTLLIKSMFTTFGMEQCRRDDYdpdsSLEYSEEETYQQFLDFYYDVLPEF-KSVGKVIQFKVSCNLEPHLRGNVYVQYQ 275
Cdd:cd12538    1 SQTILLQNLYQNPQNTPQSADGL----KVKVSDVELQEHFDEFYEDVFVELeEKYGEIEEMNVCDNLGDHLVGNVYVKFR 76
                         90       100
                 ....*....|....*....|....*...
gi 564399098 276 SEEDCQAAFSVFNGRWYAGRQLQCEFCP 303
Cdd:cd12538   77 REEDAEKAVNDLNNRWFNGQPIYAELSP 104
RRM3_RBM39_like cd12285
RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
197-301 1.86e-13

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


Pssm-ID: 409727 [Multi-domain]  Cd Length: 85  Bit Score: 65.65  E-value: 1.86e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564399098 197 SPTLLIKSMFttfgmeqcrrddyDPdssleySEEETYQQFLDFYYDVLPEFKSVGKVIQFKVSCNlepHLRGNVYVQYQS 276
Cdd:cd12285    1 SRCVILKNMF-------------DP------AEETEDNWDDEIKEDVIEECSKYGPVLHIYVDKN---SPQGNVYVKFKT 58
                         90       100
                 ....*....|....*....|....*
gi 564399098 277 EEDCQAAFSVFNGRWYAGRQLQCEF 301
Cdd:cd12285   59 IEAAQKCVQAMNGRWFDGRQITAAY 83
RRM_UHM_SPF45_PUF60 cd12374
RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar ...
238-301 3.31e-09

RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins; This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RRMs and a C-terminal UHM domain.


Pssm-ID: 409809 [Multi-domain]  Cd Length: 85  Bit Score: 53.76  E-value: 3.31e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564399098 238 DFYYDVLPEFKSVGKVIQFKVS--CNLEPHLRGNVYVQYQSEEDCQAAFSVFNGRWYAGRQLQCEF 301
Cdd:cd12374   18 DLKDEIKEECSKYGKVLNVIIHevASSEADDAVRVFVEFEDADEAIKAFRALNGRFFGGRKVKARF 83
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
242-300 1.69e-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: 48.43  E-value: 1.69e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 564399098 242 DVLPEFKSVGKVIQFKVSCNLEPHLRGNVYVQYQSEEDCQAAFSVFNGRWYAGRQLQCE 300
Cdd:cd00590   14 DLRELFSKFGEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RRM3_U2AF65 cd12232
RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
229-300 6.00e-07

RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.


Pssm-ID: 409679 [Multi-domain]  Cd Length: 89  Bit Score: 47.58  E-value: 6.00e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564399098 229 EEETYQQFLDfyyDVLPEFKSVGKVIQFKV----SCNLEPHLRGNVYVQYQSEEDCQAAFSVFNGRWYAGRQLQCE 300
Cdd:cd12232   17 DDEEYEEILE---DVKEECSKYGKVLSVVIprpeAEGVDVPGVGKVFVEFEDVEDAQKAQKALAGRKFDGRTVVAS 89
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
167-191 9.71e-06

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 42.18  E-value: 9.71e-06
                          10        20
                  ....*....|....*....|....*
gi 564399098  167 KDRANCPFYSKTGACRFGDRCSRKH 191
Cdd:pfam00642   1 YKTELCRFFLRTGYCKYGDRCKFAH 25
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
228-309 7.82e-05

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


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 45.30  E-value: 7.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564399098  228 SEEETYQQFLDFYYDVLPEFKSVGKVIQFKVscnLEPHLRGNVYVQYQSEEDCQAAFSVFNGRWYAGRQLQCEFCPVTRW 307
Cdd:TIGR01622 411 ATEEEPNWDKEIEDDVREECSKYGGVVHIYV---DDKNSAGDIYLKFDSVQAAEAAIKALNGRYFGGKMITAAFVVDAVY 487

                  ..
gi 564399098  308 KM 309
Cdd:TIGR01622 488 SK 489
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
246-301 1.93e-04

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


Pssm-ID: 409881 [Multi-domain]  Cd Length: 76  Bit Score: 40.11  E-value: 1.93e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 564399098 246 EFKSVGKVIQFKVSCNLEP-HLRGNVYVQYQSEEDCQAAFSVFNGRWYAGRQLQCEF 301
Cdd:cd12447   19 EFEKYGGVISARVITDRGSgRSKGYGYVDFATPEAAQKALAAMSGKEIDGRQINVDF 75
RRM3_HRB1_GBP2 cd21607
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, ...
241-301 4.37e-04

RNA recognition motif 3 (RRM3) 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 third RRM motif.


Pssm-ID: 410186 [Multi-domain]  Cd Length: 79  Bit Score: 39.23  E-value: 4.37e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564399098 241 YDVlpeFKSVGKVIQFKVSCNLEPHLRGNVYVQYQSEEDCQAAFSVFNGRWYAGRQLQCEF 301
Cdd:cd21607   20 YDL---FETIGKVNNAELKYDETGDPTGSAVVEYENLDDADVCISKLNNYNYGGCDLKISY 77
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
242-297 5.43e-04

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: 38.37  E-value: 5.43e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 564399098  242 DVLPEFKSVGKVIQFKVSCNLEPHLRGNVYVQYQSEEDCQAAFSVFNGRWYAGRQL 297
Cdd:pfam00076  14 DLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69
RRM_UHMK1 cd12465
RNA recognition motif (RRM) found in U2AF homology motif kinase 1 (UHMK1) and similar proteins; ...
222-303 9.07e-04

RNA recognition motif (RRM) found in U2AF homology motif kinase 1 (UHMK1) and similar proteins; This subgroup corresponds to the RRM of UHMK1. UHMK1, also termed kinase interacting with stathmin (KIS) or P-CIP2, is a serine/threonine protein kinase functionally related to RNA metabolism and neurite outgrowth. It contains an N-terminal kinase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), with high homology to the corresponding motif of the mammalian U2 small nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65 or U2AF2). UHMK1 targets two key regulators of cell proliferation and migration, the cyclin-dependent kinase (CDK) inhibitor p27Kip1 and the microtubule-destabilizing protein stathmin. It plays a critical role during vascular wound repair by preventing excessive vascular smooth muscle cell (VSMC) migration into the vascular lesion. Moreover, UHMK1 may control cell migration and neurite outgrowth by interacting with and phosphorylating the splicing factor SF1, thereby probably contributing to the control of protein expression. Furthermore, UHMK1 may be functionally related to microtubule dynamics and axon development. It localizes to RNA granules, interacts with three proteins found in RNA granules (KIF3A, NonO, and eEF1A), and further enhances the local translation. UHMK1 is highly expressed in regions of the brain implicated in schizophrenia and may play a role in susceptibility to schizophrenia.


Pssm-ID: 409898 [Multi-domain]  Cd Length: 88  Bit Score: 38.40  E-value: 9.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564399098 222 DSSLeYSEEEtyqqFLDFYYDVLPEFKSVGKVIQFKVScnLEPHLRGNVYVQYQSEEDCQAAFSVFNGRWYAGRQLQCEF 301
Cdd:cd12465   14 DSYL-QSEEE----YEDIVEDVREECQKYGPVVSLLIP--KENPGKGQVFVEYANAGDSKAAQKMLTGRMFDGKFVVATF 86

                 ..
gi 564399098 302 CP 303
Cdd:cd12465   87 YP 88
RRM1_DND1 cd12487
RNA recognition motif 1 (RRM1) found in vertebrate dead end protein homolog 1 (DND1); This ...
238-289 1.13e-03

RNA recognition motif 1 (RRM1) found in vertebrate dead end protein homolog 1 (DND1); This subgroup corresponds to the RRM1 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4, an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409913 [Multi-domain]  Cd Length: 78  Bit Score: 37.82  E-value: 1.13e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 564399098 238 DFYYDVL-PEFKSVGKVIQFKVSCNLEPHLRGNVYVQYQSEEDCQAAFSVFNG 289
Cdd:cd12487   12 DVYEDKLiPLFQSVGQLYEFRLMMTFSGLNRGFAYAKYASRRSAQAAITTLNG 64
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
234-303 4.89e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 39.49  E-value: 4.89e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564399098  234 QQFLDFYYDVLPEFKSVGKVIQFKVSCNLEPHLR----GNVYVQYQSEEDCQAAFSVFNGRWYAGRQLQCEFCP 303
Cdd:TIGR01642 427 EEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNStpgvGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYG 500
RRM3_PUB1 cd12622
RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated ...
242-299 4.98e-03

RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subfamily corresponds to the RRM3 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. 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 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: 410033 [Multi-domain]  Cd Length: 74  Bit Score: 35.89  E-value: 4.98e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 564399098 242 DVLPEFKSVGKVIQFKVSCNlephlRGNVYVQYQSEEDCQAAFSVFNGRWYAGRQLQC 299
Cdd:cd12622   16 DLIPLFQNFGVIEEVRVQRD-----KGFGFVKYDTHEEAALAIQQLNGQPFLGRPIKC 68
ZnF_C3H1 smart00356
zinc finger;
306-331 5.05e-03

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 34.53  E-value: 5.05e-03
                           10        20
                   ....*....|....*....|....*.
gi 564399098   306 RWKMAICGLFEVQQCPRGKHCNFLHV 331
Cdd:smart00356   1 KYKTELCKFFKRGYCPRGDRCKFAHP 26
RRM2_TatSF1_like cd12282
RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar ...
246-301 5.75e-03

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: 36.06  E-value: 5.75e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 564399098 246 EFKSVGKVIQFkvscnlEPHLRGNVYVQYQSEEDCQAAFSVFNGRWYAGRQLQCEF 301
Cdd:cd12282   35 KFGQVKKVVVF------DRHPDGVASVKFKEPEEADKCIQALNGRWFAGRKLEAET 84
RRM2_PUB1 cd12619
RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated ...
267-299 6.83e-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: 35.93  E-value: 6.83e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 564399098 267 RGNVYVQYQSEEDCQAAFSVFNGRWYAGRQLQC 299
Cdd:cd12619   43 RGYGFVSFRSQQDAQNAINSMNGKWLGSRPIRC 75
 
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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