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Conserved domains on  [gi|1791034383|ref|NP_001364312|]
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nuclear exosome regulator NRDE2 isoform c [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NRDE-2 pfam08424
NRDE-2, necessary for RNA interference; This is a family of eukaryotic proteins. Eukaryotic ...
 269-601 3.64e-102

NRDE-2, necessary for RNA interference; This is a family of eukaryotic proteins. Eukaryotic cells express a wide variety of endogenous small regulatory RNAs that regulate heterochromatin formation, developmental timing, defence against parasitic nucleic acids, and genome rearrangement. Many small regulatory RNAs are thought to function in nuclei, and in plants and fungi small interfering (si)RNAs associate with nascent transcripts and direct chromatin and/or DNA modifications. This family protein, NRDE-2, is required for small interfering (si)RNA-mediated silencing in nuclei. NRDE-2 associates with the Argonaute protein NRDE-3 within nuclei and is recruited by NRDE-3/siRNA complexes to nascent transcripts that have been targeted by RNA interference, RNAi, the process whereby double-stranded RNA (dsRNA) directs the sequence-specific degradation of mRNA.


:

Pssm-ID: 462472  Cd Length: 316  Bit Score: 324.66  E-value: 3.64e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1791034383  269 EFNRRVRENPWDTQLWMAFVAFQDEVMRspgiyalgEGEQEKHRKSLKLLLEKKLAV---LERAIE---SNPGSVELKLA 342
Cdd:pfam08424    1 ELNRRVKENPEDIDAWLELIEHQDTLLR--------AGSDSDRSLTKAERRALAEIKlsiLEKALKanpSNPDRERLLLG 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1791034383  343 KLQLCSEFWEPSALAKEWQKLLFLHPNNTSLWQRYLSFCQSQFGTFSVSKLHSLYGKCLSTLSAVKDGSMLSHPvlpgTE 422
Cdd:pfam08424   73 YLKEGAKIWDSKKLAKEWEELLKEHPNSIELWREYLDFRQSNFASFSVEECKEAFLKCLRTLSALLEGSKEHEA----PE 148

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1791034383  423 EAMFGLFLQQCHFLRQAGHSEKVISLFQAMVDFTFFKPDSVKELPTKVQVE-FFEPFWDSGEPRVGEKGARGWRAWMHQQ 501
Cdd:pfam08424  149 EQLLYIFLRLTRFLREAGYSELAVALWQALLELNFFRPSSLVSAPQEELLDsSFEEFWESEVPRIGEPGAKGWRHWVESR 228

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1791034383  502 ERGGWVLitpdeddEEPEEEDQEIKDKTLPRWQIWLAVERSRDQRHWRPWRpdkTKKQTEEDceDPERQVLFDDIGQSLI 581
Cdd:pfam08424  229 EGGGDAP-------EPKSDPPLEDLESRLDPFEAWAAAERSRDSKARLPAR---TMDEVEED--DPFRVVLFSDIRPFLF 296

                          330       340
                   ....*....|....*....|
gi 1791034383  582 RLSSPDLQFQLIQAFLQFLG 601
Cdd:pfam08424  297 LLPSPELKLQLVDAFLAFLG 316
NRDE2_MID super family cl41677
MTR4-interacting domain (MID) found in nuclear exosome regulator NRDE2 and similar proteins; ...
 142-213 1.42e-20

MTR4-interacting domain (MID) found in nuclear exosome regulator NRDE2 and similar proteins; NRDE2 is a protein of the nuclear speckles that regulates RNA degradation and export from the nucleus through its interaction with MTREX, an essential factor directing various RNAs to exosomal degradation. NRDE2 negatively regulates exosome functions by inhibiting the RNA helicase MTR4 recruitment and exosome interaction. This model corresponds to the N-terminal MTR4-interacting domain (MID) of NRDE2.


The actual alignment was detected with superfamily member cd22200:

Pssm-ID: 412062  Cd Length: 99  Bit Score: 87.38  E-value: 1.42e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1791034383  142 YKRKGDSCLGINPKKQCISWEGaSAAKKHSHRHLERYFTKKNVGLMRTEGIAVCSNPEP---ASSEPVTFIPVKD 213
Cdd:cd22200     26 YKRKGQSCLGLDPRKQGITWTD-SSKKKRKEKKDERYFSKASVQLLRSDGLVLSSLPKPpdaAESSSSSFIPVPD 99
 
Name Accession Description Interval E-value
NRDE-2 pfam08424
NRDE-2, necessary for RNA interference; This is a family of eukaryotic proteins. Eukaryotic ...
 269-601 3.64e-102

NRDE-2, necessary for RNA interference; This is a family of eukaryotic proteins. Eukaryotic cells express a wide variety of endogenous small regulatory RNAs that regulate heterochromatin formation, developmental timing, defence against parasitic nucleic acids, and genome rearrangement. Many small regulatory RNAs are thought to function in nuclei, and in plants and fungi small interfering (si)RNAs associate with nascent transcripts and direct chromatin and/or DNA modifications. This family protein, NRDE-2, is required for small interfering (si)RNA-mediated silencing in nuclei. NRDE-2 associates with the Argonaute protein NRDE-3 within nuclei and is recruited by NRDE-3/siRNA complexes to nascent transcripts that have been targeted by RNA interference, RNAi, the process whereby double-stranded RNA (dsRNA) directs the sequence-specific degradation of mRNA.


Pssm-ID: 462472  Cd Length: 316  Bit Score: 324.66  E-value: 3.64e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1791034383  269 EFNRRVRENPWDTQLWMAFVAFQDEVMRspgiyalgEGEQEKHRKSLKLLLEKKLAV---LERAIE---SNPGSVELKLA 342
Cdd:pfam08424    1 ELNRRVKENPEDIDAWLELIEHQDTLLR--------AGSDSDRSLTKAERRALAEIKlsiLEKALKanpSNPDRERLLLG 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1791034383  343 KLQLCSEFWEPSALAKEWQKLLFLHPNNTSLWQRYLSFCQSQFGTFSVSKLHSLYGKCLSTLSAVKDGSMLSHPvlpgTE 422
Cdd:pfam08424   73 YLKEGAKIWDSKKLAKEWEELLKEHPNSIELWREYLDFRQSNFASFSVEECKEAFLKCLRTLSALLEGSKEHEA----PE 148

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1791034383  423 EAMFGLFLQQCHFLRQAGHSEKVISLFQAMVDFTFFKPDSVKELPTKVQVE-FFEPFWDSGEPRVGEKGARGWRAWMHQQ 501
Cdd:pfam08424  149 EQLLYIFLRLTRFLREAGYSELAVALWQALLELNFFRPSSLVSAPQEELLDsSFEEFWESEVPRIGEPGAKGWRHWVESR 228

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1791034383  502 ERGGWVLitpdeddEEPEEEDQEIKDKTLPRWQIWLAVERSRDQRHWRPWRpdkTKKQTEEDceDPERQVLFDDIGQSLI 581
Cdd:pfam08424  229 EGGGDAP-------EPKSDPPLEDLESRLDPFEAWAAAERSRDSKARLPAR---TMDEVEED--DPFRVVLFSDIRPFLF 296

                          330       340
                   ....*....|....*....|
gi 1791034383  582 RLSSPDLQFQLIQAFLQFLG 601
Cdd:pfam08424  297 LLPSPELKLQLVDAFLAFLG 316
NRDE2_MID cd22200
MTR4-interacting domain (MID) found in nuclear exosome regulator NRDE2 and similar proteins; ...
 142-213 1.42e-20

MTR4-interacting domain (MID) found in nuclear exosome regulator NRDE2 and similar proteins; NRDE2 is a protein of the nuclear speckles that regulates RNA degradation and export from the nucleus through its interaction with MTREX, an essential factor directing various RNAs to exosomal degradation. NRDE2 negatively regulates exosome functions by inhibiting the RNA helicase MTR4 recruitment and exosome interaction. This model corresponds to the N-terminal MTR4-interacting domain (MID) of NRDE2.


Pssm-ID: 412062  Cd Length: 99  Bit Score: 87.38  E-value: 1.42e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1791034383  142 YKRKGDSCLGINPKKQCISWEGaSAAKKHSHRHLERYFTKKNVGLMRTEGIAVCSNPEP---ASSEPVTFIPVKD 213
Cdd:cd22200     26 YKRKGQSCLGLDPRKQGITWTD-SSKKKRKEKKDERYFSKASVQLLRSDGLVLSSLPKPpdaAESSSSSFIPVPD 99
 
Name Accession Description Interval E-value
NRDE-2 pfam08424
NRDE-2, necessary for RNA interference; This is a family of eukaryotic proteins. Eukaryotic ...
 269-601 3.64e-102

NRDE-2, necessary for RNA interference; This is a family of eukaryotic proteins. Eukaryotic cells express a wide variety of endogenous small regulatory RNAs that regulate heterochromatin formation, developmental timing, defence against parasitic nucleic acids, and genome rearrangement. Many small regulatory RNAs are thought to function in nuclei, and in plants and fungi small interfering (si)RNAs associate with nascent transcripts and direct chromatin and/or DNA modifications. This family protein, NRDE-2, is required for small interfering (si)RNA-mediated silencing in nuclei. NRDE-2 associates with the Argonaute protein NRDE-3 within nuclei and is recruited by NRDE-3/siRNA complexes to nascent transcripts that have been targeted by RNA interference, RNAi, the process whereby double-stranded RNA (dsRNA) directs the sequence-specific degradation of mRNA.


Pssm-ID: 462472  Cd Length: 316  Bit Score: 324.66  E-value: 3.64e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1791034383  269 EFNRRVRENPWDTQLWMAFVAFQDEVMRspgiyalgEGEQEKHRKSLKLLLEKKLAV---LERAIE---SNPGSVELKLA 342
Cdd:pfam08424    1 ELNRRVKENPEDIDAWLELIEHQDTLLR--------AGSDSDRSLTKAERRALAEIKlsiLEKALKanpSNPDRERLLLG 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1791034383  343 KLQLCSEFWEPSALAKEWQKLLFLHPNNTSLWQRYLSFCQSQFGTFSVSKLHSLYGKCLSTLSAVKDGSMLSHPvlpgTE 422
Cdd:pfam08424   73 YLKEGAKIWDSKKLAKEWEELLKEHPNSIELWREYLDFRQSNFASFSVEECKEAFLKCLRTLSALLEGSKEHEA----PE 148

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1791034383  423 EAMFGLFLQQCHFLRQAGHSEKVISLFQAMVDFTFFKPDSVKELPTKVQVE-FFEPFWDSGEPRVGEKGARGWRAWMHQQ 501
Cdd:pfam08424  149 EQLLYIFLRLTRFLREAGYSELAVALWQALLELNFFRPSSLVSAPQEELLDsSFEEFWESEVPRIGEPGAKGWRHWVESR 228

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1791034383  502 ERGGWVLitpdeddEEPEEEDQEIKDKTLPRWQIWLAVERSRDQRHWRPWRpdkTKKQTEEDceDPERQVLFDDIGQSLI 581
Cdd:pfam08424  229 EGGGDAP-------EPKSDPPLEDLESRLDPFEAWAAAERSRDSKARLPAR---TMDEVEED--DPFRVVLFSDIRPFLF 296

                          330       340
                   ....*....|....*....|
gi 1791034383  582 RLSSPDLQFQLIQAFLQFLG 601
Cdd:pfam08424  297 LLPSPELKLQLVDAFLAFLG 316
NRDE2_MID cd22200
MTR4-interacting domain (MID) found in nuclear exosome regulator NRDE2 and similar proteins; ...
 142-213 1.42e-20

MTR4-interacting domain (MID) found in nuclear exosome regulator NRDE2 and similar proteins; NRDE2 is a protein of the nuclear speckles that regulates RNA degradation and export from the nucleus through its interaction with MTREX, an essential factor directing various RNAs to exosomal degradation. NRDE2 negatively regulates exosome functions by inhibiting the RNA helicase MTR4 recruitment and exosome interaction. This model corresponds to the N-terminal MTR4-interacting domain (MID) of NRDE2.


Pssm-ID: 412062  Cd Length: 99  Bit Score: 87.38  E-value: 1.42e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1791034383  142 YKRKGDSCLGINPKKQCISWEGaSAAKKHSHRHLERYFTKKNVGLMRTEGIAVCSNPEP---ASSEPVTFIPVKD 213
Cdd:cd22200     26 YKRKGQSCLGLDPRKQGITWTD-SSKKKRKEKKDERYFSKASVQLLRSDGLVLSSLPKPpdaAESSSSSFIPVPD 99
 
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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