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Conserved domains on  [gi|2024504776|ref|XP_040528921|]
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nuclear exosome regulator NRDE2 isoform X2 [Gallus gallus]

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 ...
308-640 5.13e-114

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: 357.02  E-value: 5.13e-114
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  308 EHNKKVRENPRDIQAWMNFVSFQDELMRGPSPyasmGEQEVRRKSLKLILEKKLAILERAIESNPSNVD---LKLARLSV 384
Cdd:pfam08424    1 ELNRRVKENPEDIDAWLELIEHQDTLLRAGSD----SDRSLTKAERRALAEIKLSILEKALKANPSNPDrerLLLGYLKE 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  385 CTEFWESPAVIKEWQKLIFIHPNNPELWKKYLLFCQSQFSTFSVSKINSLYGKCLTTLAAVQDGSMVSHPPlpgtEEAML 464
Cdd:pfam08424   77 GAKIWDSKKLAKEWEELLKEHPNSIELWREYLDFRQSNFASFSVEECKEAFLKCLRTLSALLEGSKEHEAP----EEQLL 152
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  465 AIFIQQCHFLRQAGHSEKAVSLFQALIDFTFFKPDSVKDLPTKGQVE-FFEPFWDSGEPRIGEKGARGWRAWMHQQEKGG 543
Cdd:pfam08424  153 YIFLRLTRFLREAGYSELAVALWQALLELNFFRPSSLVSAPQEELLDsSFEEFWESEVPRIGEPGAKGWRHWVESREGGG 232
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  544 WVavdnpdddDEEEIDEDEEIKDKTLPKWHIWMDIEYSRESRHWLPWRpdkTKNQAEEDceDPERQVLFDDLGPSLIQLS 623
Cdd:pfam08424  233 DA--------PEPKSDPPLEDLESRLDPFEAWAAAERSRDSKARLPAR---TMDEVEED--DPFRVVLFSDIRPFLFLLP 299
                          330
                   ....*....|....*..
gi 2024504776  624 NPDIQHQLLYSFLQFLG 640
Cdd:pfam08424  300 SPELKLQLVDAFLAFLG 316
NRDE2_MID cd22200
MTR4-interacting domain (MID) found in nuclear exosome regulator NRDE2 and similar proteins; ...
152-244 1.70e-42

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: 150.17  E-value: 1.70e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  152 TFRIDKKSDPANWAYKSLYRGDIARYKRRGESCLGLDTKKQCIAWDSPaSEKKQLQRRPERYFSKSNVKTLNSDG--IPV 229
Cdd:cd22200      1 AFRIDRKPDPANWEYKSLYRGDIARYKRKGQSCLGLDPRKQGITWTDS-SKKKRKEKKDERYFSKASVQLLRSDGlvLSS 79
                           90
                   ....*....|....*...
gi 2024504776  230 CNKSSP---SDPAAFIPV 244
Cdd:cd22200     80 LPKPPDaaeSSSSSFIPV 97
 
Name Accession Description Interval E-value
NRDE-2 pfam08424
NRDE-2, necessary for RNA interference; This is a family of eukaryotic proteins. Eukaryotic ...
308-640 5.13e-114

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: 357.02  E-value: 5.13e-114
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  308 EHNKKVRENPRDIQAWMNFVSFQDELMRGPSPyasmGEQEVRRKSLKLILEKKLAILERAIESNPSNVD---LKLARLSV 384
Cdd:pfam08424    1 ELNRRVKENPEDIDAWLELIEHQDTLLRAGSD----SDRSLTKAERRALAEIKLSILEKALKANPSNPDrerLLLGYLKE 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  385 CTEFWESPAVIKEWQKLIFIHPNNPELWKKYLLFCQSQFSTFSVSKINSLYGKCLTTLAAVQDGSMVSHPPlpgtEEAML 464
Cdd:pfam08424   77 GAKIWDSKKLAKEWEELLKEHPNSIELWREYLDFRQSNFASFSVEECKEAFLKCLRTLSALLEGSKEHEAP----EEQLL 152
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  465 AIFIQQCHFLRQAGHSEKAVSLFQALIDFTFFKPDSVKDLPTKGQVE-FFEPFWDSGEPRIGEKGARGWRAWMHQQEKGG 543
Cdd:pfam08424  153 YIFLRLTRFLREAGYSELAVALWQALLELNFFRPSSLVSAPQEELLDsSFEEFWESEVPRIGEPGAKGWRHWVESREGGG 232
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  544 WVavdnpdddDEEEIDEDEEIKDKTLPKWHIWMDIEYSRESRHWLPWRpdkTKNQAEEDceDPERQVLFDDLGPSLIQLS 623
Cdd:pfam08424  233 DA--------PEPKSDPPLEDLESRLDPFEAWAAAERSRDSKARLPAR---TMDEVEED--DPFRVVLFSDIRPFLFLLP 299
                          330
                   ....*....|....*..
gi 2024504776  624 NPDIQHQLLYSFLQFLG 640
Cdd:pfam08424  300 SPELKLQLVDAFLAFLG 316
NRDE2_MID cd22200
MTR4-interacting domain (MID) found in nuclear exosome regulator NRDE2 and similar proteins; ...
152-244 1.70e-42

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: 150.17  E-value: 1.70e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  152 TFRIDKKSDPANWAYKSLYRGDIARYKRRGESCLGLDTKKQCIAWDSPaSEKKQLQRRPERYFSKSNVKTLNSDG--IPV 229
Cdd:cd22200      1 AFRIDRKPDPANWEYKSLYRGDIARYKRKGQSCLGLDPRKQGITWTDS-SKKKRKEKKDERYFSKASVQLLRSDGlvLSS 79
                           90
                   ....*....|....*...
gi 2024504776  230 CNKSSP---SDPAAFIPV 244
Cdd:cd22200     80 LPKPPDaaeSSSSSFIPV 97
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
311-417 3.39e-04

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 41.92  E-value: 3.39e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  311 KKVRENPRDIQAWMnfvsfqdelMRGPSpYASMGEqevrrkslkliLEKKLAILERAIESNPSNVDLKLARLSVCTEFWE 390
Cdd:COG4235      8 QALAANPNDAEGWL---------LLGRA-YLRLGR-----------YDEALAAYEKALRLDPDNADALLDLAEALLAAGD 66
                           90       100
                   ....*....|....*....|....*..
gi 2024504776  391 SPAVIKEWQKLIFIHPNNPELWkkYLL 417
Cdd:COG4235     67 TEEAEELLERALALDPDNPEAL--YLL 91
 
Name Accession Description Interval E-value
NRDE-2 pfam08424
NRDE-2, necessary for RNA interference; This is a family of eukaryotic proteins. Eukaryotic ...
308-640 5.13e-114

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: 357.02  E-value: 5.13e-114
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  308 EHNKKVRENPRDIQAWMNFVSFQDELMRGPSPyasmGEQEVRRKSLKLILEKKLAILERAIESNPSNVD---LKLARLSV 384
Cdd:pfam08424    1 ELNRRVKENPEDIDAWLELIEHQDTLLRAGSD----SDRSLTKAERRALAEIKLSILEKALKANPSNPDrerLLLGYLKE 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  385 CTEFWESPAVIKEWQKLIFIHPNNPELWKKYLLFCQSQFSTFSVSKINSLYGKCLTTLAAVQDGSMVSHPPlpgtEEAML 464
Cdd:pfam08424   77 GAKIWDSKKLAKEWEELLKEHPNSIELWREYLDFRQSNFASFSVEECKEAFLKCLRTLSALLEGSKEHEAP----EEQLL 152
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  465 AIFIQQCHFLRQAGHSEKAVSLFQALIDFTFFKPDSVKDLPTKGQVE-FFEPFWDSGEPRIGEKGARGWRAWMHQQEKGG 543
Cdd:pfam08424  153 YIFLRLTRFLREAGYSELAVALWQALLELNFFRPSSLVSAPQEELLDsSFEEFWESEVPRIGEPGAKGWRHWVESREGGG 232
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  544 WVavdnpdddDEEEIDEDEEIKDKTLPKWHIWMDIEYSRESRHWLPWRpdkTKNQAEEDceDPERQVLFDDLGPSLIQLS 623
Cdd:pfam08424  233 DA--------PEPKSDPPLEDLESRLDPFEAWAAAERSRDSKARLPAR---TMDEVEED--DPFRVVLFSDIRPFLFLLP 299
                          330
                   ....*....|....*..
gi 2024504776  624 NPDIQHQLLYSFLQFLG 640
Cdd:pfam08424  300 SPELKLQLVDAFLAFLG 316
NRDE2_MID cd22200
MTR4-interacting domain (MID) found in nuclear exosome regulator NRDE2 and similar proteins; ...
152-244 1.70e-42

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: 150.17  E-value: 1.70e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  152 TFRIDKKSDPANWAYKSLYRGDIARYKRRGESCLGLDTKKQCIAWDSPaSEKKQLQRRPERYFSKSNVKTLNSDG--IPV 229
Cdd:cd22200      1 AFRIDRKPDPANWEYKSLYRGDIARYKRKGQSCLGLDPRKQGITWTDS-SKKKRKEKKDERYFSKASVQLLRSDGlvLSS 79
                           90
                   ....*....|....*...
gi 2024504776  230 CNKSSP---SDPAAFIPV 244
Cdd:cd22200     80 LPKPPDaaeSSSSSFIPV 97
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
311-417 3.39e-04

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 41.92  E-value: 3.39e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024504776  311 KKVRENPRDIQAWMnfvsfqdelMRGPSpYASMGEqevrrkslkliLEKKLAILERAIESNPSNVDLKLARLSVCTEFWE 390
Cdd:COG4235      8 QALAANPNDAEGWL---------LLGRA-YLRLGR-----------YDEALAAYEKALRLDPDNADALLDLAEALLAAGD 66
                           90       100
                   ....*....|....*....|....*..
gi 2024504776  391 SPAVIKEWQKLIFIHPNNPELWkkYLL 417
Cdd:COG4235     67 TEEAEELLERALALDPDNPEAL--YLL 91
 
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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