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Conserved domains on  [gi|996079956|ref|NP_001307162|]
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exosome complex component CSL4 isoform 5 [Mus musculus]

Protein Classification

S1 domain-containing protein( domain architecture ID 237)

S1 domain-containing protein may bind RNA

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 ...
 10-59 3.95e-31

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: 105.02  E-value: 3.95e-31
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 996079956  10 KEDIRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSnYLLTTAENELGVV 59
Cdd:cd05791   44 KEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS-YYLSTAENELGVV 92
 
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 ...
 10-59 3.95e-31

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: 105.02  E-value: 3.95e-31
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 996079956  10 KEDIRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSnYLLTTAENELGVV 59
Cdd:cd05791   44 KEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS-YYLSTAENELGVV 92
EXOSC1 pfam10447
Exosome component EXOSC1/CSL4; This family of proteins are components of the exosome 3'->5' ...
 8-40 9.65e-10

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: 51.34  E-value: 9.65e-10
                          10        20        30
                  ....*....|....*....|....*....|...
gi 996079956    8 VSKEDIRATEKDKVEIYKSFRPGDIVLAKVISL 40
Cdd:pfam10447  80 IRSQDVRATERDRVKVIEMFRPGDIVRAQVISL 112
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 15-91 7.99e-09

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: 50.28  E-value: 7.99e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 996079956  15 ATEKDKVEIYKSFRPGDIVLAKVISLGdaqSNYLLTTAENELGVVVAH-SESGVQMVPISwCEMQCPKTHTKEFRKVA 91
Cdd:COG1096  108 VSDSYVKDLSDEFRVGDIVRAKVISTL---PPIQLSIKEPDLGVIKAKcSKCGSPLVKDG-DKLKCPNCGNVEKRKLS 181
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 22-91 1.34e-08

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 49.59  E-value: 1.34e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 996079956  22 EIYKSFRPGDIVLAKVISLGDaqsNYLLTTAENELGVVVAH-SESGVQMVPISWCEMQCPKTHTKEFRKVA 91
Cdd:PRK09521 114 SLTDAFKIGDIVRAKVISYTD---PLQLSTKGKDLGVIYAMcSRCRTPLVKKGENELKCPNCGNIETRKLS 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 ...
 10-59 3.95e-31

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: 105.02  E-value: 3.95e-31
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 996079956  10 KEDIRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSnYLLTTAENELGVV 59
Cdd:cd05791   44 KEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS-YYLSTAENELGVV 92
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 5-59 1.28e-17

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: 70.66  E-value: 1.28e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 996079956   5 SSPVSKEDIRATEKDKVEIYKSFRPGDIVLAKVISLGDAqSNYLLTTAENELGVV 59
Cdd:cd04454   29 RGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTADNELGVI 82
EXOSC1 pfam10447
Exosome component EXOSC1/CSL4; This family of proteins are components of the exosome 3'->5' ...
 8-40 9.65e-10

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: 51.34  E-value: 9.65e-10
                          10        20        30
                  ....*....|....*....|....*....|...
gi 996079956    8 VSKEDIRATEKDKVEIYKSFRPGDIVLAKVISL 40
Cdd:pfam10447  80 IRSQDVRATERDRVKVIEMFRPGDIVRAQVISL 112
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 15-91 7.99e-09

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: 50.28  E-value: 7.99e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 996079956  15 ATEKDKVEIYKSFRPGDIVLAKVISLGdaqSNYLLTTAENELGVVVAH-SESGVQMVPISwCEMQCPKTHTKEFRKVA 91
Cdd:COG1096  108 VSDSYVKDLSDEFRVGDIVRAKVISTL---PPIQLSIKEPDLGVIKAKcSKCGSPLVKDG-DKLKCPNCGNVEKRKLS 181
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 22-91 1.34e-08

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 49.59  E-value: 1.34e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 996079956  22 EIYKSFRPGDIVLAKVISLGDaqsNYLLTTAENELGVVVAH-SESGVQMVPISWCEMQCPKTHTKEFRKVA 91
Cdd:PRK09521 114 SLTDAFKIGDIVRAKVISYTD---PLQLSTKGKDLGVIYAMcSRCRTPLVKKGENELKCPNCGNIETRKLS 181
 
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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