NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|568923710|ref|XP_006501978|]
View 

pre-mRNA-splicing factor 38B isoform X2 [Mus musculus]

Protein Classification

PRP38 family protein( domain architecture ID 10505891)

pre-mRNA-splicing factor 38 (PRP38) family protein is involved in pre-mRNA splicing as a component of the spliceosome

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 2.16e-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: 2.16e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923710    1 MGLITHTDSPYIRALGFMYIRYTQPPTDLWDWFESFLDDEEDLDV--KAGGGCVMTIGEMLRSFLTKLEWFSTLFPRIPV 78
Cdd:pfam03371  81 LEYLNNEDFKYLRALGALYLRLTYPPKDVYKWLEPYLNDYRKLRIrlLDGDYKLTHMDEFVDDLLTKDRVCGTILPRLPK 160


                  ....
gi 568923710   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 ...
 265-373 2.14e-05

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: 46.42  E-value: 2.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923710  265 RRHRDDKKESKKKHSRSRSRERKH-RSRSRNAGKRSRSRSKDKSSRHKNESKEKANKRSRSGSQGRTGSVEKRKREHSPS 343
Cdd:TIGR01642   6 DREREKSRGRDRDRSSERPRRRSRdRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSV 85

                          90       100       110
                  ....*....|....*....|....*....|
gi 568923710  344 REKSRKRSRSQDRSHKREHNDSKDQSDRQD 373
Cdd:TIGR01642  86 RSIEQHRRRLRDRSPSNQWRKDDKKRSLWD 115
 
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 2.16e-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: 2.16e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923710    1 MGLITHTDSPYIRALGFMYIRYTQPPTDLWDWFESFLDDEEDLDV--KAGGGCVMTIGEMLRSFLTKLEWFSTLFPRIPV 78
Cdd:pfam03371  81 LEYLNNEDFKYLRALGALYLRLTYPPKDVYKWLEPYLNDYRKLRIrlLDGDYKLTHMDEFVDDLLTKDRVCGTILPRLPK 160


                  ....
gi 568923710   79 PVQK 82
Cdd:pfam03371 161 RIVL 164
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 265-373 2.14e-05

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: 46.42  E-value: 2.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923710  265 RRHRDDKKESKKKHSRSRSRERKH-RSRSRNAGKRSRSRSKDKSSRHKNESKEKANKRSRSGSQGRTGSVEKRKREHSPS 343
Cdd:TIGR01642   6 DREREKSRGRDRDRSSERPRRRSRdRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSV 85

                          90       100       110
                  ....*....|....*....|....*....|
gi 568923710  344 REKSRKRSRSQDRSHKREHNDSKDQSDRQD 373
Cdd:TIGR01642  86 RSIEQHRRRLRDRSPSNQWRKDDKKRSLWD 115
 
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 2.16e-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: 2.16e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923710    1 MGLITHTDSPYIRALGFMYIRYTQPPTDLWDWFESFLDDEEDLDV--KAGGGCVMTIGEMLRSFLTKLEWFSTLFPRIPV 78
Cdd:pfam03371  81 LEYLNNEDFKYLRALGALYLRLTYPPKDVYKWLEPYLNDYRKLRIrlLDGDYKLTHMDEFVDDLLTKDRVCGTILPRLPK 160


                  ....
gi 568923710   79 PVQK 82
Cdd:pfam03371 161 RIVL 164
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 265-373 2.14e-05

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: 46.42  E-value: 2.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923710  265 RRHRDDKKESKKKHSRSRSRERKH-RSRSRNAGKRSRSRSKDKSSRHKNESKEKANKRSRSGSQGRTGSVEKRKREHSPS 343
Cdd:TIGR01642   6 DREREKSRGRDRDRSSERPRRRSRdRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSV 85

                          90       100       110
                  ....*....|....*....|....*....|
gi 568923710  344 REKSRKRSRSQDRSHKREHNDSKDQSDRQD 373
Cdd:TIGR01642  86 RSIEQHRRRLRDRSPSNQWRKDDKKRSLWD 115
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 252-354 1.77e-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: 40.26  E-value: 1.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923710  252 DGEEKKHKEDKEDR-RHRDDKKESKKKHSRSRSRERKHR---------SRSRNAGKRSRSRSKDKSSRHKNESKEKANKR 321
Cdd:TIGR01642   2 DEEPDREREKSRGRdRDRSSERPRRRSRDRSRFRDRHRRsrersyredSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRR 81

                          90       100       110
                  ....*....|....*....|....*....|....
gi 568923710  322 SRSGSQGRTGsvEKRKREHSPSREKSR-KRSRSQ 354
Cdd:TIGR01642  82 SRSVRSIEQH--RRRLRDRSPSNQWRKdDKKRSL 113
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 265-370 7.44e-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: 7.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923710  265 RRHRDDKKESKKKHSRSRSRERKhRSRSRNagkrsrsrskdkssRHKNESKEKANKRSRSGSQGRTG-SVEKRKREHSPS 343
Cdd:TIGR01622   8 ERLRDSSSAGDRDRRRDKGRERS-RDRSRD--------------RERSRSRRRDRHRDRDYYRGRERrSRSRRPNRRYRP 72

                          90       100       110
                  ....*....|....*....|....*....|..
gi 568923710  344 REKSRKRS-----RSQDRSHKREHNDSKDQSD 370
Cdd:TIGR01622  73 REKRRRRGdsyrrRRDDRRSRREKPRARDGTP 104
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 280-390 7.57e-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: 7.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923710  280 RSRSRERKhRSRSRNAGKRSRSRSKDKSSRHKNESKEKANKRSRSGSQGRTGSV----EKRKREHSPsREKSRKRSRSQD 355
Cdd:TIGR01622   1 RYRDRERE-RLRDSSSAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYyrgrERRSRSRRP-NRRYRPREKRRR 78

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 568923710  356 RSHKREHNDsKDQSDRQDHQSSQSGEPESQEKEHK 390
Cdd:TIGR01622  79 RGDSYRRRR-DDRRSRREKPRARDGTPEPLTEDER 112
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 248-355 9.83e-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: 37.98  E-value: 9.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923710  248 RSRGDGEEKKHKEDKEDRRHRDDKKESKKKHSRSRSRERkHRSRSRNAGKRSRSRskdkssrhknESKEKANKRSRSGSQ 327
Cdd:TIGR01622   9 RLRDSSSAGDRDRRRDKGRERSRDRSRDRERSRSRRRDR-HRDRDYYRGRERRSR----------SRRPNRRYRPREKRR 77

                          90       100
                  ....*....|....*....|....*...
gi 568923710  328 GRTGSVEKRKREHSPSREKSRKRSRSQD 355
Cdd:TIGR01622  78 RRGDSYRRRRDDRRSRREKPRARDGTPE 105
 
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