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Conserved domains on  [gi|1944856260|ref|XP_038036938|]
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exosome complex component CSL4 [Anas platyrhynchos]

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 ...
 62-154 1.18e-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: 163.57  E-value: 1.18e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260  62 QLLPDVGAVVTCRVCSINSRFAKVHILYVGSTPLRSAFRGTIRREDIRATEKDKVEVYKSFRPGDIVLAKVISLGDAQSn 141
Cdd:cd05791     1 LVLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS- 79

                          90
                  ....*....|...
gi 1944856260 142 YLLSTAENELGVV 154
Cdd:cd05791    80 YYLSTAENELGVV 92
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 8-43 9.52e-06

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: 41.19  E-value: 9.52e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1944856260   8 CVPGERLCSAAEAAAGSGTYTRRGAVCAALAGCMRR 43
Cdd:pfam14382   2 VLPGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEI 37
 
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 ...
 62-154 1.18e-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: 163.57  E-value: 1.18e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260  62 QLLPDVGAVVTCRVCSINSRFAKVHILYVGSTPLRSAFRGTIRREDIRATEKDKVEVYKSFRPGDIVLAKVISLGDAQSn 141
Cdd:cd05791     1 LVLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS- 79

                          90
                  ....*....|...
gi 1944856260 142 YLLSTAENELGVV 154
Cdd:cd05791    80 YYLSTAENELGVV 92
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 9-186 2.77e-16

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: 73.01  E-value: 2.77e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260   9 VPGERLCSAAEAAAGSGTYTRRGAVCAALAGcmrRGGGDGGGPQVAVLRDAEAQLLPDVGAVVTCRVCSINSRFAKVHIL 88
Cdd:COG1096    10 LPGDVLAVIEEFLPGEGTYEEDGKIRAAVVG---KVVIDDKNRVISVKPKKKPPPVPKKGDIVIGEVVDVRESMALVKIY 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260  89 YV--GSTPLRSAFRGTIRREDIRATEKDKveVYKSFRPGDIVLAKVISLGdaqSNYLLSTAENELGVVVAR-SEAGVQMV 165
Cdd:COG1096    87 AIegNERELPSSFSGIIHISQVSDSYVKD--LSDEFRVGDIVRAKVISTL---PPIQLSIKEPDLGVIKAKcSKCGSPLV 161

                         170       180
                  ....*....|....*....|.
gi 1944856260 166 PISwCEMQCPQTHTKDFRKVA 186
Cdd:COG1096   162 KDG-DKLKCPNCGNVEKRKLS 181
EXOSC1 pfam10447
Exosome component EXOSC1/CSL4; This family of proteins are components of the exosome 3'->5' ...
 64-135 5.66e-13

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: 62.51  E-value: 5.66e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260  64 LPDVGAVVTCRVCSINSRFAKVHILYV---------------GSTPLRSA-------------------------FRGTI 103
Cdd:pfam10447   1 LPKEGDVVLARVTRLSQQQANVEILSVegennvlgdsgvgsnGEGAVASIpagggldilfsvstvasqssdlgetFKGII 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1944856260 104 RREDIRATEKDKVEVYKSFRPGDIVLAKVISL 135
Cdd:pfam10447  81 RSQDVRATERDRVKVIEMFRPGDIVRAQVISL 112
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 10-186 2.23e-11

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 59.99  E-value: 2.23e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260  10 PGERLCSAAEAAAGSGTYTRRGAVCAALAGCMRRGGGDGGgpqVAVLRDAEAQLLPDVGAVVTCRVCSINSRFAKVHILY 89
Cdd:PRK09521   10 PGDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIDDINRK---ISVIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVS 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260  90 V--GSTPLRSAFRGTIRREdiRATEKDKVEVYKSFRPGDIVLAKVISLGDaqsNYLLSTAENELGVVVAR-SEAGVQMVP 166
Cdd:PRK09521   87 IegSERELATSKLAYIHIS--QVSDGYVESLTDAFKIGDIVRAKVISYTD---PLQLSTKGKDLGVIYAMcSRCRTPLVK 161

                         170       180
                  ....*....|....*....|
gi 1944856260 167 ISWCEMQCPQTHTKDFRKVA 186
Cdd:PRK09521  162 KGENELKCPNCGNIETRKLS 181
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 8-43 9.52e-06

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: 41.19  E-value: 9.52e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1944856260   8 CVPGERLCSAAEAAAGSGTYTRRGAVCAALAGCMRR 43
Cdd:pfam14382   2 VLPGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEI 37
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
67-146 2.76e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 40.66  E-value: 2.76e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260   67 VGAVVTCRVCSINSRFAKVHILYVgstplrsaFRGTIRREDIraTEKDKVEVYKSFRPGDIVLAKVISLGDAQSNYLLST 146
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGNG--------VEGLIPISEL--SDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 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 ...
 62-154 1.18e-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: 163.57  E-value: 1.18e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260  62 QLLPDVGAVVTCRVCSINSRFAKVHILYVGSTPLRSAFRGTIRREDIRATEKDKVEVYKSFRPGDIVLAKVISLGDAQSn 141
Cdd:cd05791     1 LVLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS- 79

                          90
                  ....*....|...
gi 1944856260 142 YLLSTAENELGVV 154
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 ...
 62-154 6.26e-30

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: 105.32  E-value: 6.26e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260  62 QLLPDVGAVVTCRVCSINSRFAKVHILYvgstplrsafRGTIRREDIRATEKDKVEVYKSFRPGDIVLAKVISLGDAqSN 141
Cdd:cd04454     1 RYLPDVGDIVIGIVTEVNSRFWKVDILS----------RGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MN 69

                          90
                  ....*....|...
gi 1944856260 142 YLLSTAENELGVV 154
Cdd:cd04454    70 VLLTTADNELGVI 82
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 9-186 2.77e-16

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: 73.01  E-value: 2.77e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260   9 VPGERLCSAAEAAAGSGTYTRRGAVCAALAGcmrRGGGDGGGPQVAVLRDAEAQLLPDVGAVVTCRVCSINSRFAKVHIL 88
Cdd:COG1096    10 LPGDVLAVIEEFLPGEGTYEEDGKIRAAVVG---KVVIDDKNRVISVKPKKKPPPVPKKGDIVIGEVVDVRESMALVKIY 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260  89 YV--GSTPLRSAFRGTIRREDIRATEKDKveVYKSFRPGDIVLAKVISLGdaqSNYLLSTAENELGVVVAR-SEAGVQMV 165
Cdd:COG1096    87 AIegNERELPSSFSGIIHISQVSDSYVKD--LSDEFRVGDIVRAKVISTL---PPIQLSIKEPDLGVIKAKcSKCGSPLV 161

                         170       180
                  ....*....|....*....|.
gi 1944856260 166 PISwCEMQCPQTHTKDFRKVA 186
Cdd:COG1096   162 KDG-DKLKCPNCGNVEKRKLS 181
EXOSC1 pfam10447
Exosome component EXOSC1/CSL4; This family of proteins are components of the exosome 3'->5' ...
 64-135 5.66e-13

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: 62.51  E-value: 5.66e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260  64 LPDVGAVVTCRVCSINSRFAKVHILYV---------------GSTPLRSA-------------------------FRGTI 103
Cdd:pfam10447   1 LPKEGDVVLARVTRLSQQQANVEILSVegennvlgdsgvgsnGEGAVASIpagggldilfsvstvasqssdlgetFKGII 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1944856260 104 RREDIRATEKDKVEVYKSFRPGDIVLAKVISL 135
Cdd:pfam10447  81 RSQDVRATERDRVKVIEMFRPGDIVRAQVISL 112
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 10-186 2.23e-11

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 59.99  E-value: 2.23e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260  10 PGERLCSAAEAAAGSGTYTRRGAVCAALAGCMRRGGGDGGgpqVAVLRDAEAQLLPDVGAVVTCRVCSINSRFAKVHILY 89
Cdd:PRK09521   10 PGDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIDDINRK---ISVIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVS 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260  90 V--GSTPLRSAFRGTIRREdiRATEKDKVEVYKSFRPGDIVLAKVISLGDaqsNYLLSTAENELGVVVAR-SEAGVQMVP 166
Cdd:PRK09521   87 IegSERELATSKLAYIHIS--QVSDGYVESLTDAFKIGDIVRAKVISYTD---PLQLSTKGKDLGVIYAMcSRCRTPLVK 161

                         170       180
                  ....*....|....*....|
gi 1944856260 167 ISWCEMQCPQTHTKDFRKVA 186
Cdd:PRK09521  162 KGENELKCPNCGNIETRKLS 181
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 8-43 9.52e-06

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: 41.19  E-value: 9.52e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1944856260   8 CVPGERLCSAAEAAAGSGTYTRRGAVCAALAGCMRR 43
Cdd:pfam14382   2 VLPGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEI 37
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
67-146 2.76e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 40.66  E-value: 2.76e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260   67 VGAVVTCRVCSINSRFAKVHILYVgstplrsaFRGTIRREDIraTEKDKVEVYKSFRPGDIVLAKVISLGDAQSNYLLST 146
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGNG--------VEGLIPISEL--SDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 52-134 9.80e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 36.30  E-value: 9.80e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1944856260  52 QVAVLR-DAEA--------QLLPD----------VGAVVTCRVCSINSRFAKVHiLYVGSTplrsafrGTIRREDI-RAT 111
Cdd:PRK06299  426 EAVVLKvDVEKerislgikQLEEDpfeefakkhkKGSIVTGTVTEVKDKGAFVE-LEDGVE-------GLIRASELsRDR 497

                          90       100
                  ....*....|....*....|...
gi 1944856260 112 EKDKVEVYKsfrPGDIVLAKVIS 134
Cdd:PRK06299  498 VEDATEVLK---VGDEVEAKVIN 517
 
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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