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Conserved domains on  [gi|996079954|ref|NP_001307161|]
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exosome complex component CSL4 isoform 4 [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 ...
 62-137 8.94e-38

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: 125.05  E-value: 8.94e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996079954  62 QLLPDVGAVVTCKVSSINSRFAKVHILYVGSTPLKNAFRGTIRKEDIRATEKDK-----------------ISLGDAQSn 124
Cdd:cd05791    1 LVLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKvemykcfrpgdivrakvISLGDASS- 79

                         90
                 ....*....|...
gi 996079954 125 YLLTTAENELGVV 137
Cdd:cd05791   80 YYLSTAENELGVV 92
Csl4 super family cl34105
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 9-169 2.08e-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: 80.72  E-value: 2.08e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996079954   9 IPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKTSENGavpVVSVMRETESQLLPDVGAVVTCKVSSINSRFAKVHIL 88
Cdd:COG1096   10 LPGDVLAVIEEFLPGEGTYEEDGKIRAAVVGKVVIDDKNR---VISVKPKKKPPPVPKKGDIVIGEVVDVRESMALVKIY 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996079954  89 YV--GSTPLKNAFRGTIRKEDIRATEKDKIS----LGD--------AQSNYLLTTAENELGVVVAH-SESGVQMVPISwC 153
Cdd:COG1096   87 AIegNERELPSSFSGIIHISQVSDSYVKDLSdefrVGDivrakvisTLPPIQLSIKEPDLGVIKAKcSKCGSPLVKDG-D 165

                        170
                 ....*....|....*.
gi 996079954 154 EMQCPKTHTKEFRKVA 169
Cdd:COG1096  166 KLKCPNCGNVEKRKLS 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 ...
 62-137 8.94e-38

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: 125.05  E-value: 8.94e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996079954  62 QLLPDVGAVVTCKVSSINSRFAKVHILYVGSTPLKNAFRGTIRKEDIRATEKDK-----------------ISLGDAQSn 124
Cdd:cd05791    1 LVLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKvemykcfrpgdivrakvISLGDASS- 79

                         90
                 ....*....|...
gi 996079954 125 YLLTTAENELGVV 137
Cdd:cd05791   80 YYLSTAENELGVV 92
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 9-169 2.08e-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: 80.72  E-value: 2.08e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996079954   9 IPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKTSENGavpVVSVMRETESQLLPDVGAVVTCKVSSINSRFAKVHIL 88
Cdd:COG1096   10 LPGDVLAVIEEFLPGEGTYEEDGKIRAAVVGKVVIDDKNR---VISVKPKKKPPPVPKKGDIVIGEVVDVRESMALVKIY 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996079954  89 YV--GSTPLKNAFRGTIRKEDIRATEKDKIS----LGD--------AQSNYLLTTAENELGVVVAH-SESGVQMVPISwC 153
Cdd:COG1096   87 AIegNERELPSSFSGIIHISQVSDSYVKDLSdefrVGDivrakvisTLPPIQLSIKEPDLGVIKAKcSKCGSPLVKDG-D 165

                        170
                 ....*....|....*.
gi 996079954 154 EMQCPKTHTKEFRKVA 169
Cdd:COG1096  166 KLKCPNCGNVEKRKLS 181
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 10-169 5.43e-12

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 61.14  E-value: 5.43e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996079954  10 PGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKTSENgavPVVSVMRETESQLLPDVGAVVTCKVSSINSRFAKVHILY 89
Cdd:PRK09521  10 PGDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIDDIN---RKISVIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVS 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996079954  90 VG------STPLKNAFRGTIRKEDIRATEKDKISLGD--------AQSNYLLTTAENELGVVVAH-SESGVQMVPISWCE 154
Cdd:PRK09521  87 IEgserelATSKLAYIHISQVSDGYVESLTDAFKIGDivrakvisYTDPLQLSTKGKDLGVIYAMcSRCRTPLVKKGENE 166

                        170
                 ....*....|....*
gi 996079954 155 MQCPKTHTKEFRKVA 169
Cdd:PRK09521 167 LKCPNCGNIETRKLS 181
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 8-44 4.31e-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: 49.67  E-value: 4.31e-09
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 996079954    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' ...
 64-121 5.73e-04

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: 37.86  E-value: 5.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996079954   64 LPDVGAVVTCKVSSINSRFAKVHILYV---------------GSTPLKNA-------------------------FRGTI 103
Cdd:pfam10447   1 LPKEGDVVLARVTRLSQQQANVEILSVegennvlgdsgvgsnGEGAVASIpagggldilfsvstvasqssdlgetFKGII 80

                          90
                  ....*....|....*...
gi 996079954  104 RKEDIRATEKDKISLGDA 121
Cdd:pfam10447  81 RSQDVRATERDRVKVIEM 98
 
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 ...
 62-137 8.94e-38

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: 125.05  E-value: 8.94e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996079954  62 QLLPDVGAVVTCKVSSINSRFAKVHILYVGSTPLKNAFRGTIRKEDIRATEKDK-----------------ISLGDAQSn 124
Cdd:cd05791    1 LVLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKvemykcfrpgdivrakvISLGDASS- 79

                         90
                 ....*....|...
gi 996079954 125 YLLTTAENELGVV 137
Cdd:cd05791   80 YYLSTAENELGVV 92
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 9-169 2.08e-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: 80.72  E-value: 2.08e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996079954   9 IPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKTSENGavpVVSVMRETESQLLPDVGAVVTCKVSSINSRFAKVHIL 88
Cdd:COG1096   10 LPGDVLAVIEEFLPGEGTYEEDGKIRAAVVGKVVIDDKNR---VISVKPKKKPPPVPKKGDIVIGEVVDVRESMALVKIY 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996079954  89 YV--GSTPLKNAFRGTIRKEDIRATEKDKIS----LGD--------AQSNYLLTTAENELGVVVAH-SESGVQMVPISwC 153
Cdd:COG1096   87 AIegNERELPSSFSGIIHISQVSDSYVKDLSdefrVGDivrakvisTLPPIQLSIKEPDLGVIKAKcSKCGSPLVKDG-D 165

                        170
                 ....*....|....*.
gi 996079954 154 EMQCPKTHTKEFRKVA 169
Cdd:COG1096  166 KLKCPNCGNVEKRKLS 181
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 62-137 5.87e-18

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: 74.12  E-value: 5.87e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996079954  62 QLLPDVGAVVTCKVSSINSRFAKVHILYvgstplknafRGTIRKEDIRATEKDK-----------------ISLGDAqSN 124
Cdd:cd04454    1 RYLPDVGDIVIGIVTEVNSRFWKVDILS----------RGTARLEDSSATEKDKkeirkslqpgdlilakvISLGDD-MN 69

                         90
                 ....*....|...
gi 996079954 125 YLLTTAENELGVV 137
Cdd:cd04454   70 VLLTTADNELGVI 82
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 10-169 5.43e-12

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 61.14  E-value: 5.43e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996079954  10 PGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKTSENgavPVVSVMRETESQLLPDVGAVVTCKVSSINSRFAKVHILY 89
Cdd:PRK09521  10 PGDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIDDIN---RKISVIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVS 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996079954  90 VG------STPLKNAFRGTIRKEDIRATEKDKISLGD--------AQSNYLLTTAENELGVVVAH-SESGVQMVPISWCE 154
Cdd:PRK09521  87 IEgserelATSKLAYIHISQVSDGYVESLTDAFKIGDivrakvisYTDPLQLSTKGKDLGVIYAMcSRCRTPLVKKGENE 166

                        170
                 ....*....|....*
gi 996079954 155 MQCPKTHTKEFRKVA 169
Cdd:PRK09521 167 LKCPNCGNIETRKLS 181
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 8-44 4.31e-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: 49.67  E-value: 4.31e-09
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 996079954    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' ...
 64-121 5.73e-04

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: 37.86  E-value: 5.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996079954   64 LPDVGAVVTCKVSSINSRFAKVHILYV---------------GSTPLKNA-------------------------FRGTI 103
Cdd:pfam10447   1 LPKEGDVVLARVTRLSQQQANVEILSVegennvlgdsgvgsnGEGAVASIpagggldilfsvstvasqssdlgetFKGII 80

                          90
                  ....*....|....*...
gi 996079954  104 RKEDIRATEKDKISLGDA 121
Cdd:pfam10447  81 RSQDVRATERDRVKVIEM 98
 
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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