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Conserved domains on  [gi|1958668257|ref|XP_038945165|]
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zinc finger CCHC domain-containing protein 8 isoform X1 [Rattus norvegicus]

Protein Classification

zinc finger CCHC domain-containing protein( domain architecture ID 10443319)

zinc finger CCHC (ZCCHC) domain-containing protein contains a zinc knuckle or a zinc binding motif, CX2CX4HX4C, where X can be any amino acid, and may bind single-stranded RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PSP super family cl02643
PSP; Proline rich domain found in numerous spliceosome associated proteins.
 260-312 5.60e-20

PSP; Proline rich domain found in numerous spliceosome associated proteins.


The actual alignment was detected with superfamily member smart00581:

Pssm-ID: 470641  Cd Length: 54  Bit Score: 83.56  E-value: 5.60e-20
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958668257  260 FGRFKPGVISEELQDALGVTDKSLPPFIYRMRQLGYPPGWL-KEAELETSGLAL 312
Cdd:smart00581   1 FKHFKPGRISDELREALGLPPGQPPPWLYRMRRLGYPPGYPrLKIPGLNAPIPL 54
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 204-221 1.79e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


:

Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 35.97  E-value: 1.79e-03
                          10
                  ....*....|....*...
gi 1958668257 204 PHCFNCGSEEHQMKECPM 221
Cdd:pfam00098   1 GKCYNCGEPGHIARDCPK 18
COG2433 super family cl43687
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
48-110 8.73e-03

Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];


The actual alignment was detected with superfamily member COG2433:

Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 39.07  E-value: 8.73e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958668257  48 DAELQEQLRRCEETIEQLRAENQELKRKLniltrpRQYHQEIEEFVSNLvKRFEEQQKNDVEK 110
Cdd:COG2433   408 LTEEEEEIRRLEEQVERLEAEVEELEAEL------EEKDERIERLEREL-SEARSEERREIRK 463
 
Name Accession Description Interval E-value
PSP smart00581
proline-rich domain in spliceosome associated proteins;
260-312 5.60e-20

proline-rich domain in spliceosome associated proteins;


Pssm-ID: 128850  Cd Length: 54  Bit Score: 83.56  E-value: 5.60e-20
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958668257  260 FGRFKPGVISEELQDALGVTDKSLPPFIYRMRQLGYPPGWL-KEAELETSGLAL 312
Cdd:smart00581   1 FKHFKPGRISDELREALGLPPGQPPPWLYRMRRLGYPPGYPrLKIPGLNAPIPL 54
PSP pfam04046
PSP; Proline rich domain found in numerous spliceosome associated proteins.
 264-310 1.07e-17

PSP; Proline rich domain found in numerous spliceosome associated proteins.


Pssm-ID: 461145  Cd Length: 46  Bit Score: 76.71  E-value: 1.07e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1958668257 264 KPGVISEELQDALGVTDKSLPPFIYRMRQLGYPPGWlkeAELETSGL 310
Cdd:pfam04046   1 KPGKLSDELREALGLPEGQPPPWLYRMQRLGPPPSY---PNLKIPGL 44
CUS1 COG5182
Splicing factor 3b, subunit 2 [RNA processing and modification];
264-299 6.54e-04

Splicing factor 3b, subunit 2 [RNA processing and modification];


Pssm-ID: 227509 [Multi-domain]  Cd Length: 429  Bit Score: 42.67  E-value: 6.54e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958668257 264 KPGVISEELQDALGVTDKSLPPFIYRMRQLGYPPGW 299
Cdd:COG5182   279 RPGAISAELREALGIDSGTPPPWLFNMQKHGMPPSY 314
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 204-221 1.79e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 35.97  E-value: 1.79e-03
                          10
                  ....*....|....*...
gi 1958668257 204 PHCFNCGSEEHQMKECPM 221
Cdd:pfam00098   1 GKCYNCGEPGHIARDCPK 18
ZnF_C2HC smart00343
zinc finger;
206-220 2.06e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.88  E-value: 2.06e-03
                           10
                   ....*....|....*
gi 1958668257  206 CFNCGSEEHQMKECP 220
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
COG2433 COG2433
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
48-110 8.73e-03

Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];


Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 39.07  E-value: 8.73e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958668257  48 DAELQEQLRRCEETIEQLRAENQELKRKLniltrpRQYHQEIEEFVSNLvKRFEEQQKNDVEK 110
Cdd:COG2433   408 LTEEEEEIRRLEEQVERLEAEVEELEAEL------EEKDERIERLEREL-SEARSEERREIRK 463
 
Name Accession Description Interval E-value
PSP smart00581
proline-rich domain in spliceosome associated proteins;
260-312 5.60e-20

proline-rich domain in spliceosome associated proteins;


Pssm-ID: 128850  Cd Length: 54  Bit Score: 83.56  E-value: 5.60e-20
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958668257  260 FGRFKPGVISEELQDALGVTDKSLPPFIYRMRQLGYPPGWL-KEAELETSGLAL 312
Cdd:smart00581   1 FKHFKPGRISDELREALGLPPGQPPPWLYRMRRLGYPPGYPrLKIPGLNAPIPL 54
PSP pfam04046
PSP; Proline rich domain found in numerous spliceosome associated proteins.
 264-310 1.07e-17

PSP; Proline rich domain found in numerous spliceosome associated proteins.


Pssm-ID: 461145  Cd Length: 46  Bit Score: 76.71  E-value: 1.07e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1958668257 264 KPGVISEELQDALGVTDKSLPPFIYRMRQLGYPPGWlkeAELETSGL 310
Cdd:pfam04046   1 KPGKLSDELREALGLPEGQPPPWLYRMQRLGPPPSY---PNLKIPGL 44
CUS1 COG5182
Splicing factor 3b, subunit 2 [RNA processing and modification];
264-299 6.54e-04

Splicing factor 3b, subunit 2 [RNA processing and modification];


Pssm-ID: 227509 [Multi-domain]  Cd Length: 429  Bit Score: 42.67  E-value: 6.54e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958668257 264 KPGVISEELQDALGVTDKSLPPFIYRMRQLGYPPGW 299
Cdd:COG5182   279 RPGAISAELREALGIDSGTPPPWLFNMQKHGMPPSY 314
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 204-221 1.79e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 35.97  E-value: 1.79e-03
                          10
                  ....*....|....*...
gi 1958668257 204 PHCFNCGSEEHQMKECPM 221
Cdd:pfam00098   1 GKCYNCGEPGHIARDCPK 18
ZnF_C2HC smart00343
zinc finger;
206-220 2.06e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.88  E-value: 2.06e-03
                           10
                   ....*....|....*
gi 1958668257  206 CFNCGSEEHQMKECP 220
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
COG2433 COG2433
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
48-110 8.73e-03

Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];


Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 39.07  E-value: 8.73e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958668257  48 DAELQEQLRRCEETIEQLRAENQELKRKLniltrpRQYHQEIEEFVSNLvKRFEEQQKNDVEK 110
Cdd:COG2433   408 LTEEEEEIRRLEEQVERLEAEVEELEAEL------EEKDERIERLEREL-SEARSEERREIRK 463
 
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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