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Conserved domains on  [gi|1958783030|ref|XP_038968175|]
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pre-mRNA-processing factor 39 isoform X2 [Rattus norvegicus]

Protein Classification

pre-mRNA-processing factor( domain architecture ID 1007349)

pre-mRNA-processing factor similar to Candida albicans mRNA 3'-end-processing protein RNA14, a component of the cleavage factor IA (CFIA) complex, which is involved in the endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation

Gene Ontology:  GO:0071013|GO:0000398

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNA14 super family cl34906
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 67-263 3.80e-12

Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification];


The actual alignment was detected with superfamily member COG5107:

Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 68.12  E-value: 3.80e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783030  67 VTETEGNFPPEFEKFWKTVETNPQDFTGWVYLLQYVEQENHLMAARKAFDKFFIHYPYCYGYWKKYADLEKRHDNIKQSD 146
Cdd:COG5107    17 VAEPSDNIHGDELRLRERIKDNPTNILSYFQLIQYLETQESMDAEREMYEQLSSPFPIMEHAWRLYMSGELARKDFRSVE 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783030 147 EVYRRGLQAIpLSVDLWIHYINFLKETLDPGDPETNSTIRGTFEHAVLAAGTDFRSDKLWEMYIN----------WEnEQ 216
Cdd:COG5107    97 SLFGRCLKKS-LNLDLWMLYLEYIRRVNNLITGQKRFKIYEAYEFVLGCAIFEPQSENYWDEYGLfleyieelgkWE-EQ 174

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1958783030 217 GNLREVTAVYDRILGIPTQLYSHHFQRFkEHVQNNLPRdlLTGEQFI 263
Cdd:COG5107   175 QRIDKIRNGYMRALQTPMGNLEKLWKDY-ENFELELNK--ITARKFV 218
 
Name Accession Description Interval E-value
RNA14 COG5107
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 67-263 3.80e-12

Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification];


Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 68.12  E-value: 3.80e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783030  67 VTETEGNFPPEFEKFWKTVETNPQDFTGWVYLLQYVEQENHLMAARKAFDKFFIHYPYCYGYWKKYADLEKRHDNIKQSD 146
Cdd:COG5107    17 VAEPSDNIHGDELRLRERIKDNPTNILSYFQLIQYLETQESMDAEREMYEQLSSPFPIMEHAWRLYMSGELARKDFRSVE 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783030 147 EVYRRGLQAIpLSVDLWIHYINFLKETLDPGDPETNSTIRGTFEHAVLAAGTDFRSDKLWEMYIN----------WEnEQ 216
Cdd:COG5107    97 SLFGRCLKKS-LNLDLWMLYLEYIRRVNNLITGQKRFKIYEAYEFVLGCAIFEPQSENYWDEYGLfleyieelgkWE-EQ 174

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1958783030 217 GNLREVTAVYDRILGIPTQLYSHHFQRFkEHVQNNLPRdlLTGEQFI 263
Cdd:COG5107   175 QRIDKIRNGYMRALQTPMGNLEKLWKDY-ENFELELNK--ITARKFV 218
HAT smart00386
HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and ...
 141-172 6.27e-03

HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.


Pssm-ID: 214642 [Multi-domain]  Cd Length: 33  Bit Score: 34.06  E-value: 6.27e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1958783030  141 NIKQSDEVYRRGLQAIPLSVDLWIHYINFLKE 172
Cdd:smart00386   2 DIERARKIYERALEKFPKSVELWLKYAEFEER 33
 
Name Accession Description Interval E-value
RNA14 COG5107
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 67-263 3.80e-12

Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification];


Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 68.12  E-value: 3.80e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783030  67 VTETEGNFPPEFEKFWKTVETNPQDFTGWVYLLQYVEQENHLMAARKAFDKFFIHYPYCYGYWKKYADLEKRHDNIKQSD 146
Cdd:COG5107    17 VAEPSDNIHGDELRLRERIKDNPTNILSYFQLIQYLETQESMDAEREMYEQLSSPFPIMEHAWRLYMSGELARKDFRSVE 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783030 147 EVYRRGLQAIpLSVDLWIHYINFLKETLDPGDPETNSTIRGTFEHAVLAAGTDFRSDKLWEMYIN----------WEnEQ 216
Cdd:COG5107    97 SLFGRCLKKS-LNLDLWMLYLEYIRRVNNLITGQKRFKIYEAYEFVLGCAIFEPQSENYWDEYGLfleyieelgkWE-EQ 174

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1958783030 217 GNLREVTAVYDRILGIPTQLYSHHFQRFkEHVQNNLPRdlLTGEQFI 263
Cdd:COG5107   175 QRIDKIRNGYMRALQTPMGNLEKLWKDY-ENFELELNK--ITARKFV 218
HAT smart00386
HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and ...
 141-172 6.27e-03

HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.


Pssm-ID: 214642 [Multi-domain]  Cd Length: 33  Bit Score: 34.06  E-value: 6.27e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1958783030  141 NIKQSDEVYRRGLQAIPLSVDLWIHYINFLKE 172
Cdd:smart00386   2 DIERARKIYERALEKFPKSVELWLKYAEFEER 33
 
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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