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Conserved domains on  [gi|50927709|gb|AAH79122|]
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Zinc finger CCCH type containing 8 [Rattus norvegicus]

Protein Classification

zinc finger CCCH domain-containing protein( domain architecture ID 708395)

zinc finger CCCH domain-containing protein similar to cleavage and polyadenylation specificity factor (CPSF) subunit 4, which is part of the complex that plays a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YTH1 super family cl25862
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 210-282 1.87e-05

Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only];


The actual alignment was detected with superfamily member COG5084:

Pssm-ID: 227416 [Multi-domain]  Cd Length: 285  Bit Score: 45.25  E-value: 1.87e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50927709 210 VCKYFLERKCIKGDQCKFDHDAEI-EKKKEMCKYY-VQGYCTKGENCLYLHNEYP-----CKFY--HTGTKCYQGDHCNF 280
Cdd:COG5084 106 VCKFFLRGLCKSGFSCEFLHEYDLrSSQGPPCRSFsLKGSCSSGPSCGYSHIDPDsfagnCDQYsgATYGFCPLGASCKF 185


                ..
gi 50927709 281 SH 282
Cdd:COG5084 186 SH 187
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 210-282 1.87e-05

Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only];


Pssm-ID: 227416 [Multi-domain]  Cd Length: 285  Bit Score: 45.25  E-value: 1.87e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50927709 210 VCKYFLERKCIKGDQCKFDHDAEI-EKKKEMCKYY-VQGYCTKGENCLYLHNEYP-----CKFY--HTGTKCYQGDHCNF 280
Cdd:COG5084 106 VCKFFLRGLCKSGFSCEFLHEYDLrSSQGPPCRSFsLKGSCSSGPSCGYSHIDPDsfagnCDQYsgATYGFCPLGASCKF 185


                ..
gi 50927709 281 SH 282
Cdd:COG5084 186 SH 187
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 240-258 7.34e-05

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: 38.94  E-value: 7.34e-05
                          10
                  ....*....|....*....
gi 50927709   240 CKYYVQGYCTKGENCLYLH 258
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
ZnF_C3H1 smart00356
zinc finger;
240-260 2.57e-03

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 34.91  E-value: 2.57e-03
                           10        20
                   ....*....|....*....|.
gi 50927709    240 CKYYVQGYCTKGENCLYLHNE 260
Cdd:smart00356   7 CKFFKRGYCPRGDRCKFAHPL 27
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 210-282 1.87e-05

Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only];


Pssm-ID: 227416 [Multi-domain]  Cd Length: 285  Bit Score: 45.25  E-value: 1.87e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50927709 210 VCKYFLERKCIKGDQCKFDHDAEI-EKKKEMCKYY-VQGYCTKGENCLYLHNEYP-----CKFY--HTGTKCYQGDHCNF 280
Cdd:COG5084 106 VCKFFLRGLCKSGFSCEFLHEYDLrSSQGPPCRSFsLKGSCSSGPSCGYSHIDPDsfagnCDQYsgATYGFCPLGASCKF 185


                ..
gi 50927709 281 SH 282
Cdd:COG5084 186 SH 187
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 240-258 7.34e-05

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: 38.94  E-value: 7.34e-05
                          10
                  ....*....|....*....
gi 50927709   240 CKYYVQGYCTKGENCLYLH 258
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
zf-CCCH_3 pfam15663
Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically ...
 233-292 3.43e-04

Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically between 155 and 169 amino acids in length.


Pssm-ID: 464787 [Multi-domain]  Cd Length: 110  Bit Score: 39.37  E-value: 3.43e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 50927709   233 IEKKKEMCKYYVQGYCTKGENCLYLH------NEYPCKFYHTGtKCYQgDHCNFSHAPLTAETQEL 292
Cdd:pfam15663   1 MENKGDDCYFFYYSTCTKGDSCPFRHceaalgNETVCTLWQEG-RCFR-PVCRFRHMEIDKNRKEI 64
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 211-229 9.82e-04

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: 35.86  E-value: 9.82e-04
                          10
                  ....*....|....*....
gi 50927709   211 CKYFLERKCIKGDQCKFDH 229
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
zf-CCCH_3 pfam15663
Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically ...
 204-283 1.96e-03

Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically between 155 and 169 amino acids in length.


Pssm-ID: 464787 [Multi-domain]  Cd Length: 110  Bit Score: 37.44  E-value: 1.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50927709   204 ERKGKQvCKYFLERKCIKGDQCKFDHDAEIEKKKEMCKYYVQGYCTKgENCLYLH-------NEYPCKFYHTGTKCyQGD 276
Cdd:pfam15663   2 ENKGDD-CYFFYYSTCTKGDSCPFRHCEAALGNETVCTLWQEGRCFR-PVCRFRHmeidknrKEIPCYWENQPGGC-QKP 78


                  ....*..
gi 50927709   277 HCNFSHA 283
Cdd:pfam15663  79 HCAFHHT 85
ZnF_C3H1 smart00356
zinc finger;
240-260 2.57e-03

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 34.91  E-value: 2.57e-03
                           10        20
                   ....*....|....*....|.
gi 50927709    240 CKYYVQGYCTKGENCLYLHNE 260
Cdd:smart00356   7 CKFFKRGYCPRGDRCKFAHPL 27
 
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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