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Conserved domains on  [gi|1167803499|ref|NP_001336691|]
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pre-mRNA-splicing factor 38B isoform c [Homo sapiens]

Protein Classification

PRP38 family protein( domain architecture ID 3410)

PRP38 family protein similar to pre-mRNA-splicing factor 38, which is involved in pre-mRNA splicing as a component of the spliceosome

Gene Ontology:  GO:0003723|GO:0000398
SCOP:  4007353

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRP38 super family cl04030
PRP38 family; Members of this family are related to the pre mRNA splicing factor PRP38 from ...
 1-82 2.36e-34

PRP38 family; Members of this family are related to the pre mRNA splicing factor PRP38 from yeast. Therefore all the members of this family could be involved in splicing. This conserved region could be involved in RNA binding. The putative domain is about 180 amino acids in length. PRP38 is a unique component of the U4/U6.U5 tri-small nuclear ribonucleoprotein (snRNP) particle and is necessary for an essential step late in spliceosome maturation.


The actual alignment was detected with superfamily member pfam03371:

Pssm-ID: 460901  Cd Length: 165  Bit Score: 124.86  E-value: 2.36e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167803499   1 MGLITHTDSPYIRALGFMYIRYTQPPTDLWDWFESFLDDEEDLDV--KAGGGCVMTIGEMLRSFLTKLEWFSTLFPRIPV 78
Cdd:pfam03371  81 LEYLNNEDFKYLRALGALYLRLTYPPKDVYKWLEPYLNDYRKLRIrlLDGDYKLTHMDEFVDDLLTKDRVCGTILPRLPK 160


                  ....
gi 1167803499  79 PVQK 82
Cdd:pfam03371 161 RIVL 164
U2AF_lg super family cl36941
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 318-400 5.70e-04

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.


The actual alignment was detected with superfamily member TIGR01642:

Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 41.80  E-value: 5.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167803499 318 SKEKSNKRSRSGSQGRTDSVEKSKKREHSPSKEKSRKRSRSKERSHKRDHSDSKdqSDKHDRRRSQSIEQESQEKqHKNK 397
Cdd:TIGR01642  20 SSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRR--SRDRPRRRSRSVRSIEQHR-RRLR 96


                  ...
gi 1167803499 398 DET 400
Cdd:TIGR01642  97 DRS 99
 
Name Accession Description Interval E-value
PRP38 pfam03371
PRP38 family; Members of this family are related to the pre mRNA splicing factor PRP38 from ...
 1-82 2.36e-34

PRP38 family; Members of this family are related to the pre mRNA splicing factor PRP38 from yeast. Therefore all the members of this family could be involved in splicing. This conserved region could be involved in RNA binding. The putative domain is about 180 amino acids in length. PRP38 is a unique component of the U4/U6.U5 tri-small nuclear ribonucleoprotein (snRNP) particle and is necessary for an essential step late in spliceosome maturation.


Pssm-ID: 460901  Cd Length: 165  Bit Score: 124.86  E-value: 2.36e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167803499   1 MGLITHTDSPYIRALGFMYIRYTQPPTDLWDWFESFLDDEEDLDV--KAGGGCVMTIGEMLRSFLTKLEWFSTLFPRIPV 78
Cdd:pfam03371  81 LEYLNNEDFKYLRALGALYLRLTYPPKDVYKWLEPYLNDYRKLRIrlLDGDYKLTHMDEFVDDLLTKDRVCGTILPRLPK 160


                  ....
gi 1167803499  79 PVQK 82
Cdd:pfam03371 161 RIVL 164
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 318-400 5.70e-04

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: 41.80  E-value: 5.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167803499 318 SKEKSNKRSRSGSQGRTDSVEKSKKREHSPSKEKSRKRSRSKERSHKRDHSDSKdqSDKHDRRRSQSIEQESQEKqHKNK 397
Cdd:TIGR01642  20 SSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRR--SRDRPRRRSRSVRSIEQHR-RRLR 96


                  ...
gi 1167803499 398 DET 400
Cdd:TIGR01642  97 DRS 99
 
Name Accession Description Interval E-value
PRP38 pfam03371
PRP38 family; Members of this family are related to the pre mRNA splicing factor PRP38 from ...
 1-82 2.36e-34

PRP38 family; Members of this family are related to the pre mRNA splicing factor PRP38 from yeast. Therefore all the members of this family could be involved in splicing. This conserved region could be involved in RNA binding. The putative domain is about 180 amino acids in length. PRP38 is a unique component of the U4/U6.U5 tri-small nuclear ribonucleoprotein (snRNP) particle and is necessary for an essential step late in spliceosome maturation.


Pssm-ID: 460901  Cd Length: 165  Bit Score: 124.86  E-value: 2.36e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167803499   1 MGLITHTDSPYIRALGFMYIRYTQPPTDLWDWFESFLDDEEDLDV--KAGGGCVMTIGEMLRSFLTKLEWFSTLFPRIPV 78
Cdd:pfam03371  81 LEYLNNEDFKYLRALGALYLRLTYPPKDVYKWLEPYLNDYRKLRIrlLDGDYKLTHMDEFVDDLLTKDRVCGTILPRLPK 160


                  ....
gi 1167803499  79 PVQK 82
Cdd:pfam03371 161 RIVL 164
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 318-400 5.70e-04

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: 41.80  E-value: 5.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167803499 318 SKEKSNKRSRSGSQGRTDSVEKSKKREHSPSKEKSRKRSRSKERSHKRDHSDSKdqSDKHDRRRSQSIEQESQEKqHKNK 397
Cdd:TIGR01642  20 SSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRR--SRDRPRRRSRSVRSIEQHR-RRLR 96


                  ...
gi 1167803499 398 DET 400
Cdd:TIGR01642  97 DRS 99
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 338-397 3.50e-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: 3.50e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1167803499 338 EKSKKREHSPSKEKSRKRSRSKERSHKRDH---SDSKDQSDKH-DRRRSQSIEQESQEKQHKNK 397
Cdd:TIGR01642  10 EKSRGRDRDRSSERPRRRSRDRSRFRDRHRrsrERSYREDSRPrDRRRYDSRSPRSLRYSSVRR 73
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 318-397 8.57e-03

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


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 38.36  E-value: 8.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167803499 318 SKEKSNKRSRSGSQGRTDSVEKSKKREHSPSKEKSRKRS------RSKERSHKRDH--------SDSKDQSDKHDRRRSQ 383
Cdd:TIGR01622   2 YRDRERERLRDSSSAGDRDRRRDKGRERSRDRSRDRERSrsrrrdRHRDRDYYRGRerrsrsrrPNRRYRPREKRRRRGD 81

                          90
                  ....*....|....
gi 1167803499 384 SIEQESQEKQHKNK 397
Cdd:TIGR01622  82 SYRRRRDDRRSRRE 95
 
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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