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Conserved domains on  [gi|564384752|ref|XP_006251489|]
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zinc finger matrin-type protein 5 isoform X2 [Rattus norvegicus]

Protein Classification

COG5152 and zf-CCCH domain-containing protein( domain architecture ID 11893372)

COG5152 and zf-CCCH domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
54-76 1.85e-05

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


:

Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 39.87  E-value: 1.85e-05
                          10        20
                  ....*....|....*....|...
gi 564384752   54 KRPCRKFLLTGQCDFGSNCRFSH 76
Cdd:pfam00642   3 TELCRFFLRTGYCKYGDRCKFAH 25
COG5152 super family cl27117
Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function ...
 3-107 3.51e-05

Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only];


The actual alignment was detected with superfamily member COG5152:

Pssm-ID: 227481 [Multi-domain]  Cd Length: 259  Bit Score: 42.75  E-value: 3.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384752   3 KRYFCDycDRSFQDNLHNRKKHLnglqhlKAKKVWYDMFRDAaaILLDEQnKRPCRKFLLTGQCDFGSNCRFSHMSEQDL 82
Cdd:COG5152  101 KRRPSD--DNELVLNMSGKNKRL------TKQINQPTMFRDG--EVIDTQ-PDVCKDYKETGYCGYGDSCKFLHDRSDFK 169

                         90       100
                 ....*....|....*....|....*
gi 564384752  83 QGLSVQVEEERRAREWPLETAELPE 107
Cdd:COG5152  170 TGWKLNQEWNAEYEEAPVISGPGEK 194
 
Name Accession Description Interval E-value
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
54-76 1.85e-05

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 39.87  E-value: 1.85e-05
                          10        20
                  ....*....|....*....|...
gi 564384752   54 KRPCRKFLLTGQCDFGSNCRFSH 76
Cdd:pfam00642   3 TELCRFFLRTGYCKYGDRCKFAH 25
COG5152 COG5152
Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function ...
 3-107 3.51e-05

Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only];


Pssm-ID: 227481 [Multi-domain]  Cd Length: 259  Bit Score: 42.75  E-value: 3.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384752   3 KRYFCDycDRSFQDNLHNRKKHLnglqhlKAKKVWYDMFRDAaaILLDEQnKRPCRKFLLTGQCDFGSNCRFSHMSEQDL 82
Cdd:COG5152  101 KRRPSD--DNELVLNMSGKNKRL------TKQINQPTMFRDG--EVIDTQ-PDVCKDYKETGYCGYGDSCKFLHDRSDFK 169

                         90       100
                 ....*....|....*....|....*
gi 564384752  83 QGLSVQVEEERRAREWPLETAELPE 107
Cdd:COG5152  170 TGWKLNQEWNAEYEEAPVISGPGEK 194
zf-U1 pfam06220
U1 zinc finger; This family consists of several U1 small nuclear ribonucleoprotein C (U1-C) ...
 2-38 1.39e-04

U1 zinc finger; This family consists of several U1 small nuclear ribonucleoprotein C (U1-C) proteins. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site (ss) at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' ss is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' ss. Binding of TIA-1 in the vicinity of a 5' ss helps to stabilize U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator. This domain is probably a zinc-binding. It is found in multiple copies in some members of the family.


Pssm-ID: 368798  Cd Length: 38  Bit Score: 37.80  E-value: 1.39e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 564384752    2 GKRYFCDYCDRSFQDNLHN-RKKHLNGLQHLKAKKVWY 38
Cdd:pfam06220   1 MPKYYCDYCDCYLTHDSPSvRKSHNGGRKHKDNVKDYY 38
ZnF_C3H1 smart00356
zinc finger;
55-76 1.89e-03

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 34.14  E-value: 1.89e-03
                           10        20
                   ....*....|....*....|..
gi 564384752    55 RPCRKFLlTGQCDFGSNCRFSH 76
Cdd:smart00356   5 ELCKFFK-RGYCPRGDRCKFAH 25
 
Name Accession Description Interval E-value
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
54-76 1.85e-05

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 39.87  E-value: 1.85e-05
                          10        20
                  ....*....|....*....|...
gi 564384752   54 KRPCRKFLLTGQCDFGSNCRFSH 76
Cdd:pfam00642   3 TELCRFFLRTGYCKYGDRCKFAH 25
COG5152 COG5152
Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function ...
 3-107 3.51e-05

Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only];


Pssm-ID: 227481 [Multi-domain]  Cd Length: 259  Bit Score: 42.75  E-value: 3.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564384752   3 KRYFCDycDRSFQDNLHNRKKHLnglqhlKAKKVWYDMFRDAaaILLDEQnKRPCRKFLLTGQCDFGSNCRFSHMSEQDL 82
Cdd:COG5152  101 KRRPSD--DNELVLNMSGKNKRL------TKQINQPTMFRDG--EVIDTQ-PDVCKDYKETGYCGYGDSCKFLHDRSDFK 169

                         90       100
                 ....*....|....*....|....*
gi 564384752  83 QGLSVQVEEERRAREWPLETAELPE 107
Cdd:COG5152  170 TGWKLNQEWNAEYEEAPVISGPGEK 194
COG5136 COG5136
U1 snRNP-specific protein C [RNA processing and modification];
4-46 6.21e-05

U1 snRNP-specific protein C [RNA processing and modification];


Pssm-ID: 227465 [Multi-domain]  Cd Length: 188  Bit Score: 41.61  E-value: 6.21e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 564384752   4 RYFCDYCDRSF-QDNLHNRKKHLNGLQHLKAKKVWY-DMFRDAAA 46
Cdd:COG5136    3 RYFCEYCNKMLtHDRLSVRKMHCGGAKHGLMRKDYYmEMAEDIAA 47
zf-U1 pfam06220
U1 zinc finger; This family consists of several U1 small nuclear ribonucleoprotein C (U1-C) ...
 2-38 1.39e-04

U1 zinc finger; This family consists of several U1 small nuclear ribonucleoprotein C (U1-C) proteins. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site (ss) at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' ss is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' ss. Binding of TIA-1 in the vicinity of a 5' ss helps to stabilize U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator. This domain is probably a zinc-binding. It is found in multiple copies in some members of the family.


Pssm-ID: 368798  Cd Length: 38  Bit Score: 37.80  E-value: 1.39e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 564384752    2 GKRYFCDYCDRSFQDNLHN-RKKHLNGLQHLKAKKVWY 38
Cdd:pfam06220   1 MPKYYCDYCDCYLTHDSPSvRKSHNGGRKHKDNVKDYY 38
zf-CCCH_4 pfam18044
CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and ...
 55-76 3.64e-04

CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and one histidine to coordinate the zinc ion. This domain is found in a wide variety of proteins such as E3 ligases.


Pssm-ID: 465626  Cd Length: 22  Bit Score: 36.03  E-value: 3.64e-04
                          10        20
                  ....*....|....*....|..
gi 564384752   55 RPCRKFLlTGQCDFGSNCRFSH 76
Cdd:pfam18044   1 RLCRYFQ-KGGCRYGDNCRFSH 21
ZnF_C3H1 smart00356
zinc finger;
55-76 1.89e-03

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 34.14  E-value: 1.89e-03
                           10        20
                   ....*....|....*....|..
gi 564384752    55 RPCRKFLlTGQCDFGSNCRFSH 76
Cdd:smart00356   5 ELCKFFK-RGYCPRGDRCKFAH 25
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 57-76 5.92e-03

Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch domain-containing proteins such as ZIP. Functional studies indicate that ZIP specifically targets EGFR and represses its transcription, and that the zinc finger and the coiled-coil domains are central to that process.


Pssm-ID: 465719 [Multi-domain]  Cd Length: 19  Bit Score: 32.77  E-value: 5.92e-03
                          10        20
                  ....*....|....*....|
gi 564384752   57 CRKFLlTGQCDFGSNCRFSH 76
Cdd:pfam18345   1 CKFFL-KGRCRYGDKCRFAH 19
 
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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