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Conserved domains on  [gi|285813185|tpg|DAA09082|]
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TPA: Mud2p [Saccharomyces cerevisiae S288C]

Protein Classification

RNA-binding protein; RNA-binding protein 43( domain architecture ID 10647509)

RNA-binding protein containing an RNA recognition motif (RRM)| RNA-binding protein 43 (RBM43) is an RNA-binding protein containing an RNA recognition motif (RRM)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_1 smart00361
RNA recognition motif;
436-511 1.68e-15

RNA recognition motif;


:

Pssm-ID: 214637 [Multi-domain]  Cd Length: 70  Bit Score: 71.28  E-value: 1.68e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 285813185   436 KDETFITEIKETLKYSIAGADTIKICQPGVDYrlnfENLAsgAGNIYIKFKTLEAAKHAMEELPGTQFNDRTVLCT 511
Cdd:smart00361   1 KDEDFERELKEEEEYFGEVGKINKIYIDDVGY----ENHK--RGNVYITFERSEDAARAIVDLNGRYFDGRLVKAE 70
PRK12678 super family cl36163
transcription termination factor Rho; Provisional
 46-156 1.61e-03

transcription termination factor Rho; Provisional


The actual alignment was detected with superfamily member PRK12678:

Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 41.04  E-value: 1.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285813185  46 RQKSDGELPKAPKSRNVSHSNNRGPSSIITMSTNRTTYEQTRAGPHRQSYRDASGRSYNRENRYSSHNTGPQWNNNPYNR 125
Cdd:PRK12678 171 ERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDR 250

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 285813185 126 QRDERRGRNERF-------DRRGRNGNGNYDRFNYQRK 156
Cdd:PRK12678 251 DGDDGEGRGGRRgrrfrdrDRRGRRGGDGGNEREPELR 288
 
Name Accession Description Interval E-value
RRM_1 smart00361
RNA recognition motif;
436-511 1.68e-15

RNA recognition motif;


Pssm-ID: 214637 [Multi-domain]  Cd Length: 70  Bit Score: 71.28  E-value: 1.68e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 285813185   436 KDETFITEIKETLKYSIAGADTIKICQPGVDYrlnfENLAsgAGNIYIKFKTLEAAKHAMEELPGTQFNDRTVLCT 511
Cdd:smart00361   1 KDEDFERELKEEEEYFGEVGKINKIYIDDVGY----ENHK--RGNVYITFERSEDAARAIVDLNGRYFDGRLVKAE 70
RRM3_U2AF65 cd12232
RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
 436-511 9.16e-14

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: 66.84  E-value: 9.16e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 285813185 436 KDETFITEIKETLKYSIAGADTIK-ICQPGVDYRlnfENLASGAGNIYIKFKTLEAAKHAMEELPGTQFNDRTVLCT 511
Cdd:cd12232   16 EDDEEYEEILEDVKEECSKYGKVLsVVIPRPEAE---GVDVPGVGKVFVEFEDVEDAQKAQKALAGRKFDGRTVVAS 89
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 46-156 1.61e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 41.04  E-value: 1.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285813185  46 RQKSDGELPKAPKSRNVSHSNNRGPSSIITMSTNRTTYEQTRAGPHRQSYRDASGRSYNRENRYSSHNTGPQWNNNPYNR 125
Cdd:PRK12678 171 ERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDR 250

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 285813185 126 QRDERRGRNERF-------DRRGRNGNGNYDRFNYQRK 156
Cdd:PRK12678 251 DGDDGEGRGGRRgrrfrdrDRRGRRGGDGGNEREPELR 288
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 458-518 1.64e-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: 41.03  E-value: 1.64e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 285813185  458 IKICQPGVDYrlnfeNLASGAGNIYIKFKTLEAAKHAMEELPGTQFNDRTVLCTYIDEDDF 518
Cdd:TIGR01642 449 IVIPRPNGDR-----NSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGEDCY 504
 
Name Accession Description Interval E-value
RRM_1 smart00361
RNA recognition motif;
436-511 1.68e-15

RNA recognition motif;


Pssm-ID: 214637 [Multi-domain]  Cd Length: 70  Bit Score: 71.28  E-value: 1.68e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 285813185   436 KDETFITEIKETLKYSIAGADTIKICQPGVDYrlnfENLAsgAGNIYIKFKTLEAAKHAMEELPGTQFNDRTVLCT 511
Cdd:smart00361   1 KDEDFERELKEEEEYFGEVGKINKIYIDDVGY----ENHK--RGNVYITFERSEDAARAIVDLNGRYFDGRLVKAE 70
RRM3_U2AF65 cd12232
RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
 436-511 9.16e-14

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: 66.84  E-value: 9.16e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 285813185 436 KDETFITEIKETLKYSIAGADTIK-ICQPGVDYRlnfENLASGAGNIYIKFKTLEAAKHAMEELPGTQFNDRTVLCT 511
Cdd:cd12232   16 EDDEEYEEILEDVKEECSKYGKVLsVVIPRPEAE---GVDVPGVGKVFVEFEDVEDAQKAQKALAGRKFDGRTVVAS 89
RRM_U2AF35_like cd12287
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ...
 479-513 2.02e-04

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: 40.71  E-value: 2.02e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 285813185 479 GNIYIKFKTLEAAKHAMEELPGTQFNDRTVLCTYI 513
Cdd:cd12287   66 GNVYVKFESEEDAEAALQALNGRYYAGRPLYPELS 100
RRM3_RBM39_like cd12285
RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
 479-514 1.58e-03

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: 37.53  E-value: 1.58e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 285813185 479 GNIYIKFKTLEAAKHAMEELPGTQFNDRTVLCTYID 514
Cdd:cd12285   50 GNVYVKFKTIEAAQKCVQAMNGRWFDGRQITAAYVP 85
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 46-156 1.61e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 41.04  E-value: 1.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285813185  46 RQKSDGELPKAPKSRNVSHSNNRGPSSIITMSTNRTTYEQTRAGPHRQSYRDASGRSYNRENRYSSHNTGPQWNNNPYNR 125
Cdd:PRK12678 171 ERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDR 250

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 285813185 126 QRDERRGRNERF-------DRRGRNGNGNYDRFNYQRK 156
Cdd:PRK12678 251 DGDDGEGRGGRRgrrfrdrDRRGRRGGDGGNEREPELR 288
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 458-518 1.64e-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: 41.03  E-value: 1.64e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 285813185  458 IKICQPGVDYrlnfeNLASGAGNIYIKFKTLEAAKHAMEELPGTQFNDRTVLCTYIDEDDF 518
Cdd:TIGR01642 449 IVIPRPNGDR-----NSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGEDCY 504
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 45-170 1.85e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 41.04  E-value: 1.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285813185  45 KRQKSDGELPKAPKSRNVSHSNNRGPssiitmstNRTTYEQTRAGPHRQSYRDASGRSYNRENRYSSHNTGPQWNNNPYN 124
Cdd:PRK12678 140 GAARKAGEGGEQPATEARADAAERTE--------EEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQ 211

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 285813185 125 RQRDERRGRNERFDRRGRNGNGNYDRFN--YQRKNEGSKFNGDRDKRQ 170
Cdd:PRK12678 212 GDRREERGRRDGGDRRGRRRRRDRRDARgdDNREDRGDRDGDDGEGRG 259
 
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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