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Conserved domains on  [gi|257096005|ref|NP_001158033|]
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exosome complex component CSL4 isoform 2 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 74-113 7.08e-22

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05791:

Pssm-ID: 471952  Cd Length: 92  Bit Score: 83.83  E-value: 7.08e-22
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 257096005  74 KVEIYKSFRPGDIVLAKVISLGDAQSnYLLTTAENELGVV 113
Cdd:cd05791   54 KVEMYKCFRPGDIVRAKVISLGDASS-YYLSTAENELGVV 92
Csl4 super family cl34105
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 9-145 3.40e-19

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


The actual alignment was detected with superfamily member COG1096:

Pssm-ID: 440713 [Multi-domain]  Cd Length: 191  Bit Score: 79.56  E-value: 3.40e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257096005   9 IPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKTSENGavpVVSVMRETESQLLPDVGAVVTCKVE------------ 76
Cdd:COG1096   10 LPGDVLAVIEEFLPGEGTYEEDGKIRAAVVGKVVIDDKNR---VISVKPKKKPPPVPKKGDIVIGEVVdvresmalvkiy 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257096005  77 -----------------------------IYKSFRPGDIVLAKVISLGdaqSNYLLTTAENELGVVVAH-SESGVQMVPI 126
Cdd:COG1096   87 aiegnerelpssfsgiihisqvsdsyvkdLSDEFRVGDIVRAKVISTL---PPIQLSIKEPDLGVIKAKcSKCGSPLVKD 163

                        170
                 ....*....|....*....
gi 257096005 127 SwCEMQCPKTHTKEFRKVA 145
Cdd:COG1096  164 G-DKLKCPNCGNVEKRKLS 181
 
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 ...
 74-113 7.08e-22

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: 83.83  E-value: 7.08e-22
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 257096005  74 KVEIYKSFRPGDIVLAKVISLGDAQSnYLLTTAENELGVV 113
Cdd:cd05791   54 KVEMYKCFRPGDIVRAKVISLGDASS-YYLSTAENELGVV 92
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 9-145 3.40e-19

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: 79.56  E-value: 3.40e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257096005   9 IPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKTSENGavpVVSVMRETESQLLPDVGAVVTCKVE------------ 76
Cdd:COG1096   10 LPGDVLAVIEEFLPGEGTYEEDGKIRAAVVGKVVIDDKNR---VISVKPKKKPPPVPKKGDIVIGEVVdvresmalvkiy 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257096005  77 -----------------------------IYKSFRPGDIVLAKVISLGdaqSNYLLTTAENELGVVVAH-SESGVQMVPI 126
Cdd:COG1096   87 aiegnerelpssfsgiihisqvsdsyvkdLSDEFRVGDIVRAKVISTL---PPIQLSIKEPDLGVIKAKcSKCGSPLVKD 163

                        170
                 ....*....|....*....
gi 257096005 127 SwCEMQCPKTHTKEFRKVA 145
Cdd:COG1096  164 G-DKLKCPNCGNVEKRKLS 181
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 10-145 2.56e-13

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 63.84  E-value: 2.56e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257096005  10 PGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKTSENgavPVVSVMRETESQLLPDVGAVVTCKV-------------- 75
Cdd:PRK09521  10 PGDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIDDIN---RKISVIPFKKTPPLLKKGDIVYGRVvdvkeqralvrivs 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257096005  76 ---------------------------EIYKSFRPGDIVLAKVISLGDaqsNYLLTTAENELGVVVAH-SESGVQMVPIS 127
Cdd:PRK09521  87 iegserelatsklayihisqvsdgyveSLTDAFKIGDIVRAKVISYTD---PLQLSTKGKDLGVIYAMcSRCRTPLVKKG 163

                        170
                 ....*....|....*...
gi 257096005 128 WCEMQCPKTHTKEFRKVA 145
Cdd:PRK09521 164 ENELKCPNCGNIETRKLS 181
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 8-44 5.14e-09

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: 48.90  E-value: 5.14e-09
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 257096005    8 CIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKT 44
Cdd:pfam14382   2 VLPGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEIV 38
EXOSC1 pfam10447
Exosome component EXOSC1/CSL4; This family of proteins are components of the exosome 3'->5' ...
 66-94 9.05e-03

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: 34.01  E-value: 9.05e-03
                          10        20
                  ....*....|....*....|....*....
gi 257096005   66 DVGAVVTCKVEIYKSFRPGDIVLAKVISL 94
Cdd:pfam10447  84 DVRATERDRVKVIEMFRPGDIVRAQVISL 112
 
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 ...
 74-113 7.08e-22

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: 83.83  E-value: 7.08e-22
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 257096005  74 KVEIYKSFRPGDIVLAKVISLGDAQSnYLLTTAENELGVV 113
Cdd:cd05791   54 KVEMYKCFRPGDIVRAKVISLGDASS-YYLSTAENELGVV 92
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 9-145 3.40e-19

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: 79.56  E-value: 3.40e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257096005   9 IPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKTSENGavpVVSVMRETESQLLPDVGAVVTCKVE------------ 76
Cdd:COG1096   10 LPGDVLAVIEEFLPGEGTYEEDGKIRAAVVGKVVIDDKNR---VISVKPKKKPPPVPKKGDIVIGEVVdvresmalvkiy 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257096005  77 -----------------------------IYKSFRPGDIVLAKVISLGdaqSNYLLTTAENELGVVVAH-SESGVQMVPI 126
Cdd:COG1096   87 aiegnerelpssfsgiihisqvsdsyvkdLSDEFRVGDIVRAKVISTL---PPIQLSIKEPDLGVIKAKcSKCGSPLVKD 163

                        170
                 ....*....|....*....
gi 257096005 127 SwCEMQCPKTHTKEFRKVA 145
Cdd:COG1096  164 G-DKLKCPNCGNVEKRKLS 181
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 62-113 1.80e-13

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: 61.80  E-value: 1.80e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257096005  62 QLLPDVGAVVTCKV-------------------------------EIYKSFRPGDIVLAKVISLGDAqSNYLLTTAENEL 110
Cdd:cd04454    1 RYLPDVGDIVIGIVtevnsrfwkvdilsrgtarledssatekdkkEIRKSLQPGDLILAKVISLGDD-MNVLLTTADNEL 79


                 ...
gi 257096005 111 GVV 113
Cdd:cd04454   80 GVI 82
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 10-145 2.56e-13

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 63.84  E-value: 2.56e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257096005  10 PGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKTSENgavPVVSVMRETESQLLPDVGAVVTCKV-------------- 75
Cdd:PRK09521  10 PGDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIDDIN---RKISVIPFKKTPPLLKKGDIVYGRVvdvkeqralvrivs 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257096005  76 ---------------------------EIYKSFRPGDIVLAKVISLGDaqsNYLLTTAENELGVVVAH-SESGVQMVPIS 127
Cdd:PRK09521  87 iegserelatsklayihisqvsdgyveSLTDAFKIGDIVRAKVISYTD---PLQLSTKGKDLGVIYAMcSRCRTPLVKKG 163

                        170
                 ....*....|....*...
gi 257096005 128 WCEMQCPKTHTKEFRKVA 145
Cdd:PRK09521 164 ENELKCPNCGNIETRKLS 181
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 8-44 5.14e-09

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: 48.90  E-value: 5.14e-09
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 257096005    8 CIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKT 44
Cdd:pfam14382   2 VLPGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEIV 38
EXOSC1 pfam10447
Exosome component EXOSC1/CSL4; This family of proteins are components of the exosome 3'->5' ...
 66-94 9.05e-03

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: 34.01  E-value: 9.05e-03
                          10        20
                  ....*....|....*....|....*....
gi 257096005   66 DVGAVVTCKVEIYKSFRPGDIVLAKVISL 94
Cdd:pfam10447  84 DVRATERDRVKVIEMFRPGDIVRAQVISL 112
 
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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