NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1653962483|ref|NP_001357562|]
View 

pre-mRNA-processing factor 40 homolog B isoform 4 [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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRP40 super family cl34905
Splicing factor [RNA processing and modification];
111-603 4.97e-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: 174.88  E-value: 4.97e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 111 AGTGPPRALWSEHVAPDGRIYYYNADDKQSVWEKPSVLKSKAELLLSQCPWKEYKSDTGKPYYYNNQSQESRWTRPKDLD 190
Cdd:COG5104     8 MASGEARSEWEELKAPDGRIYYYNKRTGKSSWEKPKELLKGSEEDLDVDPWKECRTADGKVYYYNSITRESRWKIPPERK 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 191 DLEALVKQESAgkqqtqqlqtlqpqppqpqpdpppippgpipvpmallEPEPGRSEDCDV-LEAAQPLEQGFLQREEgps 269
Cdd:COG5104    88 KVEPIAEQKHD-------------------------------------ERSMIGGNGNDMaITDHETSEPKYLLGRL--- 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 270 SSTGQHRQPQEEEEAKpepersglswsNREKAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAY 349
Cdd:COG5104   128 MSQYGITSTKDAVYRL-----------TKEEAEKEFITMLKENQVDSTWPIFRAIEELRDPRYWMVDTDPLWRKDLFKKY 196

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 350 KAQREKEEKEEARLRAKEAKQTLQHFLEQHERMTSTTRYRRAEQTFGDLEVW-AVVPERERKEVYDDVLFFLAKKEKEQA 428
Cdd:COG5104   197 FENQEKDQREEEENKQRKYINEFCKMLAGNSHIKYYTDWFTFKSIFSKHPYYsSVVNEKTKRQTFQKYKDKLGCYEKYVG 276

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 429 KQLRRRNIQALKSILDGMSSVNFqTTWSQAQQYLMDNPSFAQDQQLQNMDKEDALICFEEHIRALEREEEEERERARLRE 508
Cdd:COG5104   277 KHMGGTALGRLEEVLRSLGSETF-IIWLLNHYVFDSVVRYLKNKEMKPLDRKDILFSFIRYVRRLEKELLSAIEERKAAA 355

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 509 RRQQRKNREAFQSFLDELHETGQLHSMSTWMELYPAVSTDVRFANMLGQPGSTPLDLFKFYVEELKARFHDEKKIIKDil 588
Cdd:COG5104   356 AQNARHHRDEFRTLLRKLYSEGKIYYRMKWKNAYPLIKDDPRFLNLLGRTGSSPLDLFFDFIVDLENMYGFARRSYER-- 433

                         490
                  ....*....|....*
gi 1653962483 589 kdrgfCVEVNTAFED 603
Cdd:COG5104   434 -----ETRTGQISPT 443
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 655-703 1.78e-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: 42.95  E-value: 1.78e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1653962483  655 FRSMLRQAVPaLELGTAWEEVRERFVCDSAFEQITLESERIRLFREFLQ 703
Cdd:smart00441   7 FKELLKEHEV-ITPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIE 54
 
Name Accession Description Interval E-value
PRP40 COG5104
Splicing factor [RNA processing and modification];
111-603 4.97e-46

Splicing factor [RNA processing and modification];


Pssm-ID: 227435 [Multi-domain]  Cd Length: 590  Bit Score: 174.88  E-value: 4.97e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 111 AGTGPPRALWSEHVAPDGRIYYYNADDKQSVWEKPSVLKSKAELLLSQCPWKEYKSDTGKPYYYNNQSQESRWTRPKDLD 190
Cdd:COG5104     8 MASGEARSEWEELKAPDGRIYYYNKRTGKSSWEKPKELLKGSEEDLDVDPWKECRTADGKVYYYNSITRESRWKIPPERK 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 191 DLEALVKQESAgkqqtqqlqtlqpqppqpqpdpppippgpipvpmallEPEPGRSEDCDV-LEAAQPLEQGFLQREEgps 269
Cdd:COG5104    88 KVEPIAEQKHD-------------------------------------ERSMIGGNGNDMaITDHETSEPKYLLGRL--- 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 270 SSTGQHRQPQEEEEAKpepersglswsNREKAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAY 349
Cdd:COG5104   128 MSQYGITSTKDAVYRL-----------TKEEAEKEFITMLKENQVDSTWPIFRAIEELRDPRYWMVDTDPLWRKDLFKKY 196

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 350 KAQREKEEKEEARLRAKEAKQTLQHFLEQHERMTSTTRYRRAEQTFGDLEVW-AVVPERERKEVYDDVLFFLAKKEKEQA 428
Cdd:COG5104   197 FENQEKDQREEEENKQRKYINEFCKMLAGNSHIKYYTDWFTFKSIFSKHPYYsSVVNEKTKRQTFQKYKDKLGCYEKYVG 276

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 429 KQLRRRNIQALKSILDGMSSVNFqTTWSQAQQYLMDNPSFAQDQQLQNMDKEDALICFEEHIRALEREEEEERERARLRE 508
Cdd:COG5104   277 KHMGGTALGRLEEVLRSLGSETF-IIWLLNHYVFDSVVRYLKNKEMKPLDRKDILFSFIRYVRRLEKELLSAIEERKAAA 355

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 509 RRQQRKNREAFQSFLDELHETGQLHSMSTWMELYPAVSTDVRFANMLGQPGSTPLDLFKFYVEELKARFHDEKKIIKDil 588
Cdd:COG5104   356 AQNARHHRDEFRTLLRKLYSEGKIYYRMKWKNAYPLIKDDPRFLNLLGRTGSSPLDLFFDFIVDLENMYGFARRSYER-- 433

                         490
                  ....*....|....*
gi 1653962483 589 kdrgfCVEVNTAFED 603
Cdd:COG5104   434 -----ETRTGQISPT 443
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 300-349 4.26e-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: 4.26e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1653962483 300 KAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAY 349
Cdd:pfam01846   1 KAREAFKELLKEHKITPYSTWSEIKKKIENDPRYKALLDGSEREELFEDY 50
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 159-188 2.33e-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: 2.33e-08
                          10        20        30
                  ....*....|....*....|....*....|
gi 1653962483 159 CPWKEYKSDTGKPYYYNNQSQESRWTRPKD 188
Cdd:cd00201     2 PGWEERWDPDGRVYYYNHNTKETQWEDPRE 31
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 299-352 2.62e-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: 51.04  E-value: 2.62e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1653962483  299 EKAKQAFKELLRDKAVP-SNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAYKAQ 352
Cdd:smart00441   1 EEAKEAFKELLKEHEVItPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIEE 55
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 655-703 1.78e-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: 42.95  E-value: 1.78e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1653962483  655 FRSMLRQAVPaLELGTAWEEVRERFVCDSAFEQITLESERIRLFREFLQ 703
Cdd:smart00441   7 FKELLKEHEV-ITPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIE 54
 
Name Accession Description Interval E-value
PRP40 COG5104
Splicing factor [RNA processing and modification];
111-603 4.97e-46

Splicing factor [RNA processing and modification];


Pssm-ID: 227435 [Multi-domain]  Cd Length: 590  Bit Score: 174.88  E-value: 4.97e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 111 AGTGPPRALWSEHVAPDGRIYYYNADDKQSVWEKPSVLKSKAELLLSQCPWKEYKSDTGKPYYYNNQSQESRWTRPKDLD 190
Cdd:COG5104     8 MASGEARSEWEELKAPDGRIYYYNKRTGKSSWEKPKELLKGSEEDLDVDPWKECRTADGKVYYYNSITRESRWKIPPERK 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 191 DLEALVKQESAgkqqtqqlqtlqpqppqpqpdpppippgpipvpmallEPEPGRSEDCDV-LEAAQPLEQGFLQREEgps 269
Cdd:COG5104    88 KVEPIAEQKHD-------------------------------------ERSMIGGNGNDMaITDHETSEPKYLLGRL--- 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 270 SSTGQHRQPQEEEEAKpepersglswsNREKAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAY 349
Cdd:COG5104   128 MSQYGITSTKDAVYRL-----------TKEEAEKEFITMLKENQVDSTWPIFRAIEELRDPRYWMVDTDPLWRKDLFKKY 196

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 350 KAQREKEEKEEARLRAKEAKQTLQHFLEQHERMTSTTRYRRAEQTFGDLEVW-AVVPERERKEVYDDVLFFLAKKEKEQA 428
Cdd:COG5104   197 FENQEKDQREEEENKQRKYINEFCKMLAGNSHIKYYTDWFTFKSIFSKHPYYsSVVNEKTKRQTFQKYKDKLGCYEKYVG 276

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 429 KQLRRRNIQALKSILDGMSSVNFqTTWSQAQQYLMDNPSFAQDQQLQNMDKEDALICFEEHIRALEREEEEERERARLRE 508
Cdd:COG5104   277 KHMGGTALGRLEEVLRSLGSETF-IIWLLNHYVFDSVVRYLKNKEMKPLDRKDILFSFIRYVRRLEKELLSAIEERKAAA 355

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1653962483 509 RRQQRKNREAFQSFLDELHETGQLHSMSTWMELYPAVSTDVRFANMLGQPGSTPLDLFKFYVEELKARFHDEKKIIKDil 588
Cdd:COG5104   356 AQNARHHRDEFRTLLRKLYSEGKIYYRMKWKNAYPLIKDDPRFLNLLGRTGSSPLDLFFDFIVDLENMYGFARRSYER-- 433

                         490
                  ....*....|....*
gi 1653962483 589 kdrgfCVEVNTAFED 603
Cdd:COG5104   434 -----ETRTGQISPT 443
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 300-349 4.26e-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: 4.26e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1653962483 300 KAKQAFKELLRDKAVPSNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAY 349
Cdd:pfam01846   1 KAREAFKELLKEHKITPYSTWSEIKKKIENDPRYKALLDGSEREELFEDY 50
WW pfam00397
WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds ...
 120-145 1.96e-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: 1.96e-08
                          10        20
                  ....*....|....*....|....*.
gi 1653962483 120 WSEHVAPDGRIYYYNADDKQSVWEKP 145
Cdd:pfam00397   5 WEERWDPDGRVYYYNHETGETQWEKP 30
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 159-188 2.33e-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: 2.33e-08
                          10        20        30
                  ....*....|....*....|....*....|
gi 1653962483 159 CPWKEYKSDTGKPYYYNNQSQESRWTRPKD 188
Cdd:cd00201     2 PGWEERWDPDGRVYYYNHNTKETQWEDPRE 31
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 299-352 2.62e-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: 51.04  E-value: 2.62e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1653962483  299 EKAKQAFKELLRDKAVP-SNASWEQAMKMVVTDPRYSALPKLSEKKQAFNAYKAQ 352
Cdd:smart00441   1 EEAKEAFKELLKEHEVItPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIEE 55
WW pfam00397
WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds ...
 160-186 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 1653962483 160 PWKEYKSDTGKPYYYNNQSQESRWTRP 186
Cdd:pfam00397   4 GWEERWDPDGRVYYYNHETGETQWEKP 30
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 120-145 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 1653962483 120 WSEHVAPDGRIYYYNADDKQSVWEKP 145
Cdd:cd00201     4 WEERWDPDGRVYYYNHNTKETQWEDP 29
WW smart00456
Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds ...
 160-188 2.14e-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: 2.14e-07
                           10        20
                   ....*....|....*....|....*....
gi 1653962483  160 PWKEYKSDTGKPYYYNNQSQESRWTRPKD 188
Cdd:smart00456   5 GWEERKDPDGRPYYYNHETKETQWEKPRE 33
WW smart00456
Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds ...
 120-145 4.00e-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: 4.00e-07
                           10        20
                   ....*....|....*....|....*.
gi 1653962483  120 WSEHVAPDGRIYYYNADDKQSVWEKP 145
Cdd:smart00456   6 WEERKDPDGRPYYYNHETKETQWEKP 31
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 514-569 1.95e-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: 45.53  E-value: 1.95e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1653962483 514 KNREAFQSFLDELHetgqLHSMSTWMELYPAVSTDVRFANMlgQPGSTPLDLFKFY 569
Cdd:pfam01846   1 KAREAFKELLKEHK----ITPYSTWSEIKKKIENDPRYKAL--LDGSEREELFEDY 50
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 655-703 1.78e-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: 42.95  E-value: 1.78e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1653962483  655 FRSMLRQAVPaLELGTAWEEVRERFVCDSAFEQITLESERIRLFREFLQ 703
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH