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Conserved domains on  [gi|998701112|ref|XP_015488212|]
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exosome complex component CSL4 isoform X2 [Parus major]

Protein Classification

ECR1_N and S1_CSL4 domain-containing protein( domain architecture ID 10627461)

ECR1_N and S1_CSL4 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1_CSL4 cd05791
S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 79-171 7.29e-52

S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


:

Pssm-ID: 240217  Cd Length: 92  Bit Score: 162.03  E-value: 7.29e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998701112  79 QLLPNVGAVVTCKVCSINSRFAKVHILYVGSTPLKSTFRGTIRREDIRATEKDKVEVYKSFRPSDIVLAKVISLGDAQSn 158
Cdd:cd05791    1 LVLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS- 79

                         90
                 ....*....|...
gi 998701112 159 YLLSTAENELGVV 171
Cdd:cd05791   80 YYLSTAENELGVV 92
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 25-61 8.69e-10

Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.


:

Pssm-ID: 464162 [Multi-domain]  Cd Length: 38  Bit Score: 52.36  E-value: 8.69e-10
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 998701112   25 CVAGERLCSTEEATAGSGTYTRHGFIFSSLAGCLERK 61
Cdd:pfam14382   2 VLPGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEIV 38
 
Name Accession Description Interval E-value
S1_CSL4 cd05791
S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 79-171 7.29e-52

S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240217  Cd Length: 92  Bit Score: 162.03  E-value: 7.29e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998701112  79 QLLPNVGAVVTCKVCSINSRFAKVHILYVGSTPLKSTFRGTIRREDIRATEKDKVEVYKSFRPSDIVLAKVISLGDAQSn 158
Cdd:cd05791    1 LVLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS- 79

                         90
                 ....*....|...
gi 998701112 159 YLLSTAENELGVV 171
Cdd:cd05791   80 YYLSTAENELGVV 92
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 28-203 8.71e-27

Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440713 [Multi-domain]  Cd Length: 191  Bit Score: 101.13  E-value: 8.71e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998701112  28 GERLCSTEEATAGSGTYTRHGFIFSSLAGCLERKNEDNelpVVSVVRDSESQLLPNVGAVVTCKVCSINSRFAKVHILYV 107
Cdd:COG1096   12 GDVLAVIEEFLPGEGTYEEDGKIRAAVVGKVVIDDKNR---VISVKPKKKPPPVPKKGDIVIGEVVDVRESMALVKIYAI 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998701112 108 --GSTPLKSTFRGTIRREDIRATEKDKVevYKSFRPSDIVLAKVISLGdaqSNYLLSTAENELGVVVAR-SEAGVQMVPI 184
Cdd:COG1096   89 egNERELPSSFSGIIHISQVSDSYVKDL--SDEFRVGDIVRAKVISTL---PPIQLSIKEPDLGVIKAKcSKCGSPLVKD 163

                        170
                 ....*....|....*....
gi 998701112 185 SwCEMQCPRTHTKEFRKVA 203
Cdd:COG1096  164 G-DKLKCPNCGNVEKRKLS 181
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 28-203 1.81e-17

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 76.55  E-value: 1.81e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998701112  28 GERLCSTEEATAGSGTYTRHGFIFSSLAGCLERKNEDNElpvVSVVRDSESQLLPNVGAVVTCKVCSINSRFAKVHILYV 107
Cdd:PRK09521  11 GDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIDDINRK---ISVIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSI 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998701112 108 --GSTPLKSTFRGTIRREdiRATEKDKVEVYKSFRPSDIVLAKVISLGDaqsNYLLSTAENELGVVVAR-SEAGVQMVPI 184
Cdd:PRK09521  88 egSERELATSKLAYIHIS--QVSDGYVESLTDAFKIGDIVRAKVISYTD---PLQLSTKGKDLGVIYAMcSRCRTPLVKK 162

                        170
                 ....*....|....*....
gi 998701112 185 SWCEMQCPRTHTKEFRKVA 203
Cdd:PRK09521 163 GENELKCPNCGNIETRKLS 181
EXOSC1 pfam10447
Exosome component EXOSC1/CSL4; This family of proteins are components of the exosome 3'->5' ...
 81-152 3.88e-12

Exosome component EXOSC1/CSL4; This family of proteins are components of the exosome 3'->5' exoribonuclease complex. The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions.


Pssm-ID: 402191  Cd Length: 112  Bit Score: 60.59  E-value: 3.88e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998701112   81 LPNVGAVVTCKVCSINSRFAKVHILYV---------------GSTPLKS-------------------------TFRGTI 120
Cdd:pfam10447   1 LPKEGDVVLARVTRLSQQQANVEILSVegennvlgdsgvgsnGEGAVASipagggldilfsvstvasqssdlgeTFKGII 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 998701112  121 RREDIRATEKDKVEVYKSFRPSDIVLAKVISL 152
Cdd:pfam10447  81 RSQDVRATERDRVKVIEMFRPGDIVRAQVISL 112
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 25-61 8.69e-10

Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.


Pssm-ID: 464162 [Multi-domain]  Cd Length: 38  Bit Score: 52.36  E-value: 8.69e-10
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 998701112   25 CVAGERLCSTEEATAGSGTYTRHGFIFSSLAGCLERK 61
Cdd:pfam14382   2 VLPGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEIV 38
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
83-163 8.12e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 36.81  E-value: 8.12e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998701112    83 NVGAVVTCKVCSINSRFAKVHILyvgstplkSTFRGTIRREDIraTEKDKVEVYKSFRPSDIVLAKVISLGDAQSNYLLS 162
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLG--------NGVEGLIPISEL--SDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70


                   .
gi 998701112   163 T 163
Cdd:smart00316  71 L 71
 
Name Accession Description Interval E-value
S1_CSL4 cd05791
S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 79-171 7.29e-52

S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240217  Cd Length: 92  Bit Score: 162.03  E-value: 7.29e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998701112  79 QLLPNVGAVVTCKVCSINSRFAKVHILYVGSTPLKSTFRGTIRREDIRATEKDKVEVYKSFRPSDIVLAKVISLGDAQSn 158
Cdd:cd05791    1 LVLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS- 79

                         90
                 ....*....|...
gi 998701112 159 YLLSTAENELGVV 171
Cdd:cd05791   80 YYLSTAENELGVV 92
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 79-171 9.23e-28

S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 239901 [Multi-domain]  Cd Length: 82  Bit Score: 100.32  E-value: 9.23e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998701112  79 QLLPNVGAVVTCKVCSINSRFAKVHILYvgstplkstfRGTIRREDIRATEKDKVEVYKSFRPSDIVLAKVISLGDAqSN 158
Cdd:cd04454    1 RYLPDVGDIVIGIVTEVNSRFWKVDILS----------RGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MN 69

                         90
                 ....*....|...
gi 998701112 159 YLLSTAENELGVV 171
Cdd:cd04454   70 VLLTTADNELGVI 82
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 28-203 8.71e-27

Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440713 [Multi-domain]  Cd Length: 191  Bit Score: 101.13  E-value: 8.71e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998701112  28 GERLCSTEEATAGSGTYTRHGFIFSSLAGCLERKNEDNelpVVSVVRDSESQLLPNVGAVVTCKVCSINSRFAKVHILYV 107
Cdd:COG1096   12 GDVLAVIEEFLPGEGTYEEDGKIRAAVVGKVVIDDKNR---VISVKPKKKPPPVPKKGDIVIGEVVDVRESMALVKIYAI 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998701112 108 --GSTPLKSTFRGTIRREDIRATEKDKVevYKSFRPSDIVLAKVISLGdaqSNYLLSTAENELGVVVAR-SEAGVQMVPI 184
Cdd:COG1096   89 egNERELPSSFSGIIHISQVSDSYVKDL--SDEFRVGDIVRAKVISTL---PPIQLSIKEPDLGVIKAKcSKCGSPLVKD 163

                        170
                 ....*....|....*....
gi 998701112 185 SwCEMQCPRTHTKEFRKVA 203
Cdd:COG1096  164 G-DKLKCPNCGNVEKRKLS 181
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 28-203 1.81e-17

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 76.55  E-value: 1.81e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998701112  28 GERLCSTEEATAGSGTYTRHGFIFSSLAGCLERKNEDNElpvVSVVRDSESQLLPNVGAVVTCKVCSINSRFAKVHILYV 107
Cdd:PRK09521  11 GDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIDDINRK---ISVIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSI 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998701112 108 --GSTPLKSTFRGTIRREdiRATEKDKVEVYKSFRPSDIVLAKVISLGDaqsNYLLSTAENELGVVVAR-SEAGVQMVPI 184
Cdd:PRK09521  88 egSERELATSKLAYIHIS--QVSDGYVESLTDAFKIGDIVRAKVISYTD---PLQLSTKGKDLGVIYAMcSRCRTPLVKK 162

                        170
                 ....*....|....*....
gi 998701112 185 SWCEMQCPRTHTKEFRKVA 203
Cdd:PRK09521 163 GENELKCPNCGNIETRKLS 181
EXOSC1 pfam10447
Exosome component EXOSC1/CSL4; This family of proteins are components of the exosome 3'->5' ...
 81-152 3.88e-12

Exosome component EXOSC1/CSL4; This family of proteins are components of the exosome 3'->5' exoribonuclease complex. The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions.


Pssm-ID: 402191  Cd Length: 112  Bit Score: 60.59  E-value: 3.88e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998701112   81 LPNVGAVVTCKVCSINSRFAKVHILYV---------------GSTPLKS-------------------------TFRGTI 120
Cdd:pfam10447   1 LPKEGDVVLARVTRLSQQQANVEILSVegennvlgdsgvgsnGEGAVASipagggldilfsvstvasqssdlgeTFKGII 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 998701112  121 RREDIRATEKDKVEVYKSFRPSDIVLAKVISL 152
Cdd:pfam10447  81 RSQDVRATERDRVKVIEMFRPGDIVRAQVISL 112
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 25-61 8.69e-10

Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.


Pssm-ID: 464162 [Multi-domain]  Cd Length: 38  Bit Score: 52.36  E-value: 8.69e-10
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 998701112   25 CVAGERLCSTEEATAGSGTYTRHGFIFSSLAGCLERK 61
Cdd:pfam14382   2 VLPGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEIV 38
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
83-163 8.12e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 36.81  E-value: 8.12e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998701112    83 NVGAVVTCKVCSINSRFAKVHILyvgstplkSTFRGTIRREDIraTEKDKVEVYKSFRPSDIVLAKVISLGDAQSNYLLS 162
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLG--------NGVEGLIPISEL--SDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70


                   .
gi 998701112   163 T 163
Cdd:smart00316  71 L 71
 
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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