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Conserved domains on  [gi|9055244|ref|NP_061256|]
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pre-mRNA-processing factor 40 homolog B isoform 2 [Mus musculus]

Protein Classification

pre-mRNA-processing factor 40 family protein( domain architecture ID 13418230)

pre-mRNA-processing factor 40 (PRPF40) family protein similar to mammalian PRPF40 homologs A and B that may be involved in pre-mRNA splicing; contains WW and FF domains

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRP40 super family cl34905
Splicing factor [RNA processing and modification];
89-581 6.77e-46

Splicing factor [RNA processing and modification];


The actual alignment was detected with superfamily member COG5104:

Pssm-ID: 227435 [Multi-domain]  Cd Length: 590  Bit Score: 174.50  E-value: 6.77e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244   89 AGTGPPRALWSEHVAPDGRIYYYNADDKQSVWEKPSVLKSKAELLLSQCPWKEYKSDTGKPYYYNNQSQESRWTRPKDLD 168
Cdd:COG5104   8 MASGEARSEWEELKAPDGRIYYYNKRTGKSSWEKPKELLKGSEEDLDVDPWKECRTADGKVYYYNSITRESRWKIPPERK 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244  169 DLEALVKQESAgkqqtqqlqtlqpqppqpqpdpppippgpipvpmallEPEPGRSEDCDV-LEAAQPLEQGFLQREEgps 247
Cdd:COG5104  88 KVEPIAEQKHD-------------------------------------ERSMIGGNGNDMaITDHETSEPKYLLGRL--- 127

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244  248 SSTGQHRQPQEEEEAKpepersglswsNREKAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAY 327
Cdd:COG5104 128 MSQYGITSTKDAVYRL-----------TKEEAEKEFITMLKENQVDSTWPIFRAIEELRDPRYWMVDTDPLWRKDLFKKY 196

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244  328 KAQREKEEKEEARLRAKEAKQTLQHFLEQHERMTSTTRYRRAEQTFGDLEVW-AVVPERERKEVYDDVLFFLAKKEKEQA 406
Cdd:COG5104 197 FENQEKDQREEEENKQRKYINEFCKMLAGNSHIKYYTDWFTFKSIFSKHPYYsSVVNEKTKRQTFQKYKDKLGCYEKYVG 276

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244  407 KQLRRRNIQALKSILDGMSSVNFqTTWSQAQQYLMDNPSFAQDQQLQNMDKEDALICFEEHIRALEREEEEERERARLRE 486
Cdd:COG5104 277 KHMGGTALGRLEEVLRSLGSETF-IIWLLNHYVFDSVVRYLKNKEMKPLDRKDILFSFIRYVRRLEKELLSAIEERKAAA 355

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244  487 RRQQRKNREAFQSFLDELHETGQLHSMSTWMELYPAVSTDVRFANMLGQPGSTPLDLFKFYVEELKARFHDEKKIIKDil 566
Cdd:COG5104 356 AQNARHHRDEFRTLLRKLYSEGKIYYRMKWKNAYPLIKDDPRFLNLLGRTGSSPLDLFFDFIVDLENMYGFARRSYER-- 433

                       490
                ....*....|....*
gi 9055244  567 kdrgfCVEVNTAFED 581
Cdd:COG5104 434 -----ETRTGQISPT 443
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 633-681 2.07e-05

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


:

Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 42.56  E-value: 2.07e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 9055244     633 FRSMLRQAVPaLELGTAWEEVRERFVCDSAFEQITLESERIRLFREFLQ 681
Cdd:smart00441   7 FKELLKEHEV-ITPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIE 54
 
Name Accession Description Interval E-value
PRP40 COG5104
Splicing factor [RNA processing and modification];
89-581 6.77e-46

Splicing factor [RNA processing and modification];


Pssm-ID: 227435 [Multi-domain]  Cd Length: 590  Bit Score: 174.50  E-value: 6.77e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244   89 AGTGPPRALWSEHVAPDGRIYYYNADDKQSVWEKPSVLKSKAELLLSQCPWKEYKSDTGKPYYYNNQSQESRWTRPKDLD 168
Cdd:COG5104   8 MASGEARSEWEELKAPDGRIYYYNKRTGKSSWEKPKELLKGSEEDLDVDPWKECRTADGKVYYYNSITRESRWKIPPERK 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244  169 DLEALVKQESAgkqqtqqlqtlqpqppqpqpdpppippgpipvpmallEPEPGRSEDCDV-LEAAQPLEQGFLQREEgps 247
Cdd:COG5104  88 KVEPIAEQKHD-------------------------------------ERSMIGGNGNDMaITDHETSEPKYLLGRL--- 127

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244  248 SSTGQHRQPQEEEEAKpepersglswsNREKAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAY 327
Cdd:COG5104 128 MSQYGITSTKDAVYRL-----------TKEEAEKEFITMLKENQVDSTWPIFRAIEELRDPRYWMVDTDPLWRKDLFKKY 196

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244  328 KAQREKEEKEEARLRAKEAKQTLQHFLEQHERMTSTTRYRRAEQTFGDLEVW-AVVPERERKEVYDDVLFFLAKKEKEQA 406
Cdd:COG5104 197 FENQEKDQREEEENKQRKYINEFCKMLAGNSHIKYYTDWFTFKSIFSKHPYYsSVVNEKTKRQTFQKYKDKLGCYEKYVG 276

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244  407 KQLRRRNIQALKSILDGMSSVNFqTTWSQAQQYLMDNPSFAQDQQLQNMDKEDALICFEEHIRALEREEEEERERARLRE 486
Cdd:COG5104 277 KHMGGTALGRLEEVLRSLGSETF-IIWLLNHYVFDSVVRYLKNKEMKPLDRKDILFSFIRYVRRLEKELLSAIEERKAAA 355

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244  487 RRQQRKNREAFQSFLDELHETGQLHSMSTWMELYPAVSTDVRFANMLGQPGSTPLDLFKFYVEELKARFHDEKKIIKDil 566
Cdd:COG5104 356 AQNARHHRDEFRTLLRKLYSEGKIYYRMKWKNAYPLIKDDPRFLNLLGRTGSSPLDLFFDFIVDLENMYGFARRSYER-- 433

                       490
                ....*....|....*
gi 9055244  567 kdrgfCVEVNTAFED 581
Cdd:COG5104 434 -----ETRTGQISPT 443
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 278-327 4.86e-14

FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.


Pssm-ID: 426471 [Multi-domain]  Cd Length: 50  Bit Score: 67.10  E-value: 4.86e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 9055244    278 KAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAY 327
Cdd:pfam01846   1 KAREAFKELLKEHKITPYSTWSEIKKKIENDPRYKALLDGSEREELFEDY 50
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 137-166 2.32e-08

Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.


Pssm-ID: 238122 [Multi-domain]  Cd Length: 31  Bit Score: 50.22  E-value: 2.32e-08
                        10        20        30
                ....*....|....*....|....*....|
gi 9055244  137 CPWKEYKSDTGKPYYYNNQSQESRWTRPKD 166
Cdd:cd00201   2 PGWEERWDPDGRVYYYNHNTKETQWEDPRE 31
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 277-330 3.14e-08

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 50.65  E-value: 3.14e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 9055244     277 EKAKQAFKELLRDKAVP-SNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAYKAQ 330
Cdd:smart00441   1 EEAKEAFKELLKEHEVItPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIEE 55
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 633-681 2.07e-05

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 42.56  E-value: 2.07e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 9055244     633 FRSMLRQAVPaLELGTAWEEVRERFVCDSAFEQITLESERIRLFREFLQ 681
Cdd:smart00441   7 FKELLKEHEV-ITPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIE 54
 
Name Accession Description Interval E-value
PRP40 COG5104
Splicing factor [RNA processing and modification];
89-581 6.77e-46

Splicing factor [RNA processing and modification];


Pssm-ID: 227435 [Multi-domain]  Cd Length: 590  Bit Score: 174.50  E-value: 6.77e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244   89 AGTGPPRALWSEHVAPDGRIYYYNADDKQSVWEKPSVLKSKAELLLSQCPWKEYKSDTGKPYYYNNQSQESRWTRPKDLD 168
Cdd:COG5104   8 MASGEARSEWEELKAPDGRIYYYNKRTGKSSWEKPKELLKGSEEDLDVDPWKECRTADGKVYYYNSITRESRWKIPPERK 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244  169 DLEALVKQESAgkqqtqqlqtlqpqppqpqpdpppippgpipvpmallEPEPGRSEDCDV-LEAAQPLEQGFLQREEgps 247
Cdd:COG5104  88 KVEPIAEQKHD-------------------------------------ERSMIGGNGNDMaITDHETSEPKYLLGRL--- 127

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244  248 SSTGQHRQPQEEEEAKpepersglswsNREKAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAY 327
Cdd:COG5104 128 MSQYGITSTKDAVYRL-----------TKEEAEKEFITMLKENQVDSTWPIFRAIEELRDPRYWMVDTDPLWRKDLFKKY 196

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244  328 KAQREKEEKEEARLRAKEAKQTLQHFLEQHERMTSTTRYRRAEQTFGDLEVW-AVVPERERKEVYDDVLFFLAKKEKEQA 406
Cdd:COG5104 197 FENQEKDQREEEENKQRKYINEFCKMLAGNSHIKYYTDWFTFKSIFSKHPYYsSVVNEKTKRQTFQKYKDKLGCYEKYVG 276

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244  407 KQLRRRNIQALKSILDGMSSVNFqTTWSQAQQYLMDNPSFAQDQQLQNMDKEDALICFEEHIRALEREEEEERERARLRE 486
Cdd:COG5104 277 KHMGGTALGRLEEVLRSLGSETF-IIWLLNHYVFDSVVRYLKNKEMKPLDRKDILFSFIRYVRRLEKELLSAIEERKAAA 355

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9055244  487 RRQQRKNREAFQSFLDELHETGQLHSMSTWMELYPAVSTDVRFANMLGQPGSTPLDLFKFYVEELKARFHDEKKIIKDil 566
Cdd:COG5104 356 AQNARHHRDEFRTLLRKLYSEGKIYYRMKWKNAYPLIKDDPRFLNLLGRTGSSPLDLFFDFIVDLENMYGFARRSYER-- 433

                       490
                ....*....|....*
gi 9055244  567 kdrgfCVEVNTAFED 581
Cdd:COG5104 434 -----ETRTGQISPT 443
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 278-327 4.86e-14

FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.


Pssm-ID: 426471 [Multi-domain]  Cd Length: 50  Bit Score: 67.10  E-value: 4.86e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 9055244    278 KAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAY 327
Cdd:pfam01846   1 KAREAFKELLKEHKITPYSTWSEIKKKIENDPRYKALLDGSEREELFEDY 50
WW pfam00397
WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds ...
 98-123 1.93e-08

WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.


Pssm-ID: 459800 [Multi-domain]  Cd Length: 30  Bit Score: 50.58  E-value: 1.93e-08
                          10        20
                  ....*....|....*....|....*.
gi 9055244     98 WSEHVAPDGRIYYYNADDKQSVWEKP 123
Cdd:pfam00397   5 WEERWDPDGRVYYYNHETGETQWEKP 30
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 137-166 2.32e-08

Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.


Pssm-ID: 238122 [Multi-domain]  Cd Length: 31  Bit Score: 50.22  E-value: 2.32e-08
                        10        20        30
                ....*....|....*....|....*....|
gi 9055244  137 CPWKEYKSDTGKPYYYNNQSQESRWTRPKD 166
Cdd:cd00201   2 PGWEERWDPDGRVYYYNHNTKETQWEDPRE 31
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 277-330 3.14e-08

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 50.65  E-value: 3.14e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 9055244     277 EKAKQAFKELLRDKAVP-SNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAYKAQ 330
Cdd:smart00441   1 EEAKEAFKELLKEHEVItPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIEE 55
WW pfam00397
WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds ...
 138-164 1.18e-07

WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.


Pssm-ID: 459800 [Multi-domain]  Cd Length: 30  Bit Score: 48.27  E-value: 1.18e-07
                          10        20
                  ....*....|....*....|....*..
gi 9055244    138 PWKEYKSDTGKPYYYNNQSQESRWTRP 164
Cdd:pfam00397   4 GWEERWDPDGRVYYYNHETGETQWEKP 30
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 98-123 1.68e-07

Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.


Pssm-ID: 238122 [Multi-domain]  Cd Length: 31  Bit Score: 47.91  E-value: 1.68e-07
                        10        20
                ....*....|....*....|....*.
gi 9055244   98 WSEHVAPDGRIYYYNADDKQSVWEKP 123
Cdd:cd00201   4 WEERWDPDGRVYYYNHNTKETQWEDP 29
WW smart00456
Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds ...
 138-166 2.06e-07

Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.


Pssm-ID: 197736 [Multi-domain]  Cd Length: 33  Bit Score: 47.60  E-value: 2.06e-07
                           10        20
                   ....*....|....*....|....*....
gi 9055244     138 PWKEYKSDTGKPYYYNNQSQESRWTRPKD 166
Cdd:smart00456   5 GWEERKDPDGRPYYYNHETKETQWEKPRE 33
WW smart00456
Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds ...
 98-123 3.90e-07

Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.


Pssm-ID: 197736 [Multi-domain]  Cd Length: 33  Bit Score: 46.83  E-value: 3.90e-07
                           10        20
                   ....*....|....*....|....*.
gi 9055244      98 WSEHVAPDGRIYYYNADDKQSVWEKP 123
Cdd:smart00456   6 WEERKDPDGRPYYYNHETKETQWEKP 31
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 492-547 2.08e-06

FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.


Pssm-ID: 426471 [Multi-domain]  Cd Length: 50  Bit Score: 45.14  E-value: 2.08e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 9055244    492 KNREAFQSFLDELHetgqLHSMSTWMELYPAVSTDVRFANMlgQPGSTPLDLFKFY 547
Cdd:pfam01846   1 KAREAFKELLKEHK----ITPYSTWSEIKKKIENDPRYKAL--LDGSEREELFEDY 50
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 633-681 2.07e-05

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 42.56  E-value: 2.07e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 9055244     633 FRSMLRQAVPaLELGTAWEEVRERFVCDSAFEQITLESERIRLFREFLQ 681
Cdd:smart00441   7 FKELLKEHEV-ITPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIE 54
 
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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