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Conserved domains on  [gi|1720404732|ref|XP_030108621|]
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pre-mRNA-splicing factor 38B isoform X4 [Mus musculus]

Protein Classification

splicing factor U2AF large subunit( domain architecture ID 1002097)

splicing factor U2AF large subunit such as U2AF65, also termed U2AF2, which 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

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 ...
 1-30 1.36e-05

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: 44.74  E-value: 1.36e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 1720404732   1 MTIGEMLRSFLTKLEWFSTLFPRIPVPVQK 30
Cdd:pfam03371 135 THMDEFVDDLLTKDRVCGTILPRLPKRIVL 164
U2AF_lg super family cl36941
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 213-321 8.80e-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: 44.11  E-value: 8.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720404732 213 RRHRDDKKESKKKHSRSRSRERKH-RSRSRNAGKRSRSRSKDKSSRHKNESKEKANKRSRSGSQGRTGSVEKRKREHSPS 291
Cdd:TIGR01642   6 DREREKSRGRDRDRSSERPRRRSRdRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSV 85

                          90       100       110
                  ....*....|....*....|....*....|
gi 1720404732 292 REKSRKRSRSQDRSHKREHNDSKDQSDRQD 321
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 ...
 1-30 1.36e-05

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: 44.74  E-value: 1.36e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 1720404732   1 MTIGEMLRSFLTKLEWFSTLFPRIPVPVQK 30
Cdd:pfam03371 135 THMDEFVDDLLTKDRVCGTILPRLPKRIVL 164
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 213-321 8.80e-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: 44.11  E-value: 8.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720404732 213 RRHRDDKKESKKKHSRSRSRERKH-RSRSRNAGKRSRSRSKDKSSRHKNESKEKANKRSRSGSQGRTGSVEKRKREHSPS 291
Cdd:TIGR01642   6 DREREKSRGRDRDRSSERPRRRSRdRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSV 85

                          90       100       110
                  ....*....|....*....|....*....|
gi 1720404732 292 REKSRKRSRSQDRSHKREHNDSKDQSDRQD 321
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 ...
 1-30 1.36e-05

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: 44.74  E-value: 1.36e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 1720404732   1 MTIGEMLRSFLTKLEWFSTLFPRIPVPVQK 30
Cdd:pfam03371 135 THMDEFVDDLLTKDRVCGTILPRLPKRIVL 164
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 213-321 8.80e-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: 44.11  E-value: 8.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720404732 213 RRHRDDKKESKKKHSRSRSRERKH-RSRSRNAGKRSRSRSKDKSSRHKNESKEKANKRSRSGSQGRTGSVEKRKREHSPS 291
Cdd:TIGR01642   6 DREREKSRGRDRDRSSERPRRRSRdRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSV 85

                          90       100       110
                  ....*....|....*....|....*....|
gi 1720404732 292 REKSRKRSRSQDRSHKREHNDSKDQSDRQD 321
Cdd:TIGR01642  86 RSIEQHRRRLRDRSPSNQWRKDDKKRSLWD 115
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 200-304 7.91e-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: 37.95  E-value: 7.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720404732 200 DGEEKKHKEDKEDR-RHRDDKKESKKKHSRSRSRERKHR---------SRSRNAGKRSRSRSKDKSSRHKNESKEKANKR 269
Cdd:TIGR01642   2 DEEPDREREKSRGRdRDRSSERPRRRSRDRSRFRDRHRRsrersyredSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRR 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1720404732 270 SRSGSQGRTGSVEKRKREHSPSREKSRKRSRSQDR 304
Cdd:TIGR01642  82 SRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLWDI 116
 
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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