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Conserved domains on  [gi|568913492|ref|XP_006498007|]
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exosome complex component RRP4 isoform X1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KH-I_Rrp4_eukar cd22525
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from ...
 57-173 2.12e-60

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from eukaryote; The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from eukaryote. Rrp4, also called exosome component 2 (EXOSC2), or ribosomal RNA-processing protein 4, is a non-catalytic component of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Mutations in EXOSC2 gene are associated with a novel syndrome characterized by retinitis pigmentosa, progressive hearing loss, premature aging, short stature, mild intellectual disability and distinctive gestalt. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


:

Pssm-ID: 411953  Cd Length: 123  Bit Score: 183.62  E-value: 2.12e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568913492  57 GVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWIYPTPEHKDEDAGGFIA----NLEPVALSDREVISRLRNCVVLL 132
Cdd:cd22525    1 GILVKVPPSLIKRQKSHFHNLPCGVDVILGLNGYIWISPTVEESGEEAGGSAAiysnNNEPVSPETREAIARVRNCIKAL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 568913492 133 VTQRMMLFDTSILYCYEASL--AHQIKDILKPEVMEEIMLETR 173
Cdd:cd22525   81 AALHIPITDTSILAVYEASLelGIEVKDLLKPEVMEEIVEEAR 123
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 2-54 7.39e-19

S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 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 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: 240215 [Multi-domain]  Cd Length: 86  Bit Score: 76.43  E-value: 7.39e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 568913492   2 NLPGGE-LRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKL 54
Cdd:cd05789   33 VLPLSEvNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRSLKYGKL 86
 
Name Accession Description Interval E-value
KH-I_Rrp4_eukar cd22525
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from ...
 57-173 2.12e-60

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from eukaryote; The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from eukaryote. Rrp4, also called exosome component 2 (EXOSC2), or ribosomal RNA-processing protein 4, is a non-catalytic component of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Mutations in EXOSC2 gene are associated with a novel syndrome characterized by retinitis pigmentosa, progressive hearing loss, premature aging, short stature, mild intellectual disability and distinctive gestalt. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411953  Cd Length: 123  Bit Score: 183.62  E-value: 2.12e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568913492  57 GVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWIYPTPEHKDEDAGGFIA----NLEPVALSDREVISRLRNCVVLL 132
Cdd:cd22525    1 GILVKVPPSLIKRQKSHFHNLPCGVDVILGLNGYIWISPTVEESGEEAGGSAAiysnNNEPVSPETREAIARVRNCIKAL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 568913492 133 VTQRMMLFDTSILYCYEASL--AHQIKDILKPEVMEEIMLETR 173
Cdd:cd22525   81 AALHIPITDTSILAVYEASLelGIEVKDLLKPEVMEEIVEEAR 123
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 2-54 7.39e-19

S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 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 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: 240215 [Multi-domain]  Cd Length: 86  Bit Score: 76.43  E-value: 7.39e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 568913492   2 NLPGGE-LRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKL 54
Cdd:cd05789   33 VLPLSEvNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRSLKYGKL 86
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 57-99 1.05e-10

KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause para-neoplastic opsoclonus ataxia.


Pssm-ID: 464959 [Multi-domain]  Cd Length: 47  Bit Score: 54.36  E-value: 1.05e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 568913492   57 GVLVQVSPSLVKRQKTHF--HDLPC--GASVILGNNGFIWIYPTPEH 99
Cdd:pfam15985   1 GMLVKVSLSLVRRLLKSHflHELGKkgPFEIAVGLNGRIWIKSETVK 47
PRK04163 PRK04163
exosome complex protein Rrp4;
3-102 1.48e-05

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 43.73  E-value: 1.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568913492   3 LPGGE-LRRRSAEDELAMRGFLQEGDLISAEVQAV--FSDGAVSLHTRSLkyGKLGQGVLVQVSPSLVKR---------- 69
Cdd:PRK04163  91 LPVSEvLGRPVNVEGTDLRKYLDIGDYIIAKVKDVdrTRDVVLTLKGKGL--GKIEGGTIVEIKPVKVPRvigkkgsmin 168

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 568913492  70 ---QKThfhdlpcGASVILGNNGFIWIYPTPEHKDE 102
Cdd:PRK04163 169 mlkEET-------GCDIIVGQNGRIWIKGPDEEDEE 197
 
Name Accession Description Interval E-value
KH-I_Rrp4_eukar cd22525
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from ...
 57-173 2.12e-60

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from eukaryote; The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from eukaryote. Rrp4, also called exosome component 2 (EXOSC2), or ribosomal RNA-processing protein 4, is a non-catalytic component of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Mutations in EXOSC2 gene are associated with a novel syndrome characterized by retinitis pigmentosa, progressive hearing loss, premature aging, short stature, mild intellectual disability and distinctive gestalt. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411953  Cd Length: 123  Bit Score: 183.62  E-value: 2.12e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568913492  57 GVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWIYPTPEHKDEDAGGFIA----NLEPVALSDREVISRLRNCVVLL 132
Cdd:cd22525    1 GILVKVPPSLIKRQKSHFHNLPCGVDVILGLNGYIWISPTVEESGEEAGGSAAiysnNNEPVSPETREAIARVRNCIKAL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 568913492 133 VTQRMMLFDTSILYCYEASL--AHQIKDILKPEVMEEIMLETR 173
Cdd:cd22525   81 AALHIPITDTSILAVYEASLelGIEVKDLLKPEVMEEIVEEAR 123
KH-I_Rrp4_Rrp40 cd22445
type I K homology (KH) RNA-binding domain found in exosome complex components Rrp4, Rrp40 and ...
 57-149 4.76e-28

type I K homology (KH) RNA-binding domain found in exosome complex components Rrp4, Rrp40 and similar proteins; The family includes two ribosomal RNA-processing proteins, Rrp4 and Rrp40. They are non-catalytic components of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Eukaryotic Rrp4 and Rrp40 contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411873 [Multi-domain]  Cd Length: 78  Bit Score: 100.03  E-value: 4.76e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568913492  57 GVLVQVSPSLVKRQKT------HFHDLPCGASVILGNNGFIWIYPTPehkdedaggfianlepvalsdREVISRLRNCVV 130
Cdd:cd22445    1 GLLVKVTPGLVRRLLApdceiiQEVGKLYPLEIVFGMNGRIWVKAKT---------------------RQQTSILANIIE 59

                         90
                 ....*....|....*....
gi 568913492 131 LLVTQRMMLFDTSILYCYE 149
Cdd:cd22445   60 ACEHMHTSDQRKQIFSRLA 78
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 2-54 7.39e-19

S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 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 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: 240215 [Multi-domain]  Cd Length: 86  Bit Score: 76.43  E-value: 7.39e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 568913492   2 NLPGGE-LRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKL 54
Cdd:cd05789   33 VLPLSEvNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRSLKYGKL 86
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 15-54 3.83e-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: 3.83e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 568913492  15 DELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKL 54
Cdd:cd04454   43 DKKEIRKSLQPGDLILAKVISLGDDMNVLLTTADNELGVI 82
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 57-99 1.05e-10

KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause para-neoplastic opsoclonus ataxia.


Pssm-ID: 464959 [Multi-domain]  Cd Length: 47  Bit Score: 54.36  E-value: 1.05e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 568913492   57 GVLVQVSPSLVKRQKTHF--HDLPC--GASVILGNNGFIWIYPTPEH 99
Cdd:pfam15985   1 GMLVKVSLSLVRRLLKSHflHELGKkgPFEIAVGLNGRIWIKSETVK 47
PRK04163 PRK04163
exosome complex protein Rrp4;
3-102 1.48e-05

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 43.73  E-value: 1.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568913492   3 LPGGE-LRRRSAEDELAMRGFLQEGDLISAEVQAV--FSDGAVSLHTRSLkyGKLGQGVLVQVSPSLVKR---------- 69
Cdd:PRK04163  91 LPVSEvLGRPVNVEGTDLRKYLDIGDYIIAKVKDVdrTRDVVLTLKGKGL--GKIEGGTIVEIKPVKVPRvigkkgsmin 168

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 568913492  70 ---QKThfhdlpcGASVILGNNGFIWIYPTPEHKDE 102
Cdd:PRK04163 169 mlkEET-------GCDIIVGQNGRIWIKGPDEEDEE 197
 
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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