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Conserved domains on  [gi|1609559042|ref|NP_001356369|]
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zinc finger protein 286A isoform 4 [Homo sapiens]

Protein Classification

KRAB domain-containing zinc finger protein( domain architecture ID 12204268)

KRAB (Kruppel-associated box) domain-containing zinc finger protein (KRAB-ZFP) plays important roles in cell differentiation and organ development, and in regulating viral replication and transcription

CATH:  3.30.160.60
Gene Ontology:  GO:0003700|GO:0046872
PubMed:  22803940
SCOP:  4003583

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
1-47 7.25e-18

krueppel associated box;


:

Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 77.25  E-value: 7.25e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1609559042    1 MDFTPEEWGKLDPAQ----RDVMLENYRNLVSLWLPVSKPE-SYNLENGKEP 47
Cdd:smart00349   8 VYFTQEEWEQLDPAQknlyRDVMLENYSNLVSLGFQVPKPDlISQLEQGEEP 59
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
301-456 2.49e-07

FOG: Zn-finger [General function prediction only];


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 52.78  E-value: 2.49e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559042 301 KPYECNECDKAFIHSSALIKHQRT--HTGE--KPYKC--QECGKAFSHCSSLTKHQRVHTGEKPYEC--SECGKTFSQST 372
Cdd:COG5048   288 LPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEklLNSSSKFSPLL 367

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559042 373 H-----LVQHQRIHTGEKPYEC--NECGKTFSRSSNFAKHQRIHIGKKP--YKCSECGKAFIHSSALIQHQRTHTGEKPF 443
Cdd:COG5048   368 NneppqSLQQYKDLKNDKKSETlsNSCIRNFKRDSNLSLHIITHLSFRPynCKNPPCSKSFNRHYNLIPHKKIHTNHAPL 447

                         170
                  ....*....|...
gi 1609559042 444 RCNECGKSFKCSS 456
Cdd:COG5048   448 LCSILKSFRRDLD 460
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
171-310 2.56e-05

FOG: Zn-finger [General function prediction only];


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 46.61  E-value: 2.56e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559042 171 KSLKQKSNLMKKQR----TYKEKKPHKC--NDCGELFTYHSVLIRHQRVHTGEKPYTC--NECGKSFS------HRANLT 236
Cdd:COG5048   297 ISFSRSSPLTRHLRsvnhSGESLKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEklLNSSSKFSpllnnePPQSLQ 376

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1609559042 237 KHQRTHTRILFEC--SECKKTFTESSSLATHQRIHVGERPYECN--ECGKGFNRSTHLVQHQLIHTGVKPYECNECDK 310
Cdd:COG5048   377 QYKDLKNDKKSETlsNSCIRNFKRDSNLSLHIITHLSFRPYNCKnpPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKS 454
 
Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
1-47 7.25e-18

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 77.25  E-value: 7.25e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1609559042    1 MDFTPEEWGKLDPAQ----RDVMLENYRNLVSLWLPVSKPE-SYNLENGKEP 47
Cdd:smart00349   8 VYFTQEEWEQLDPAQknlyRDVMLENYSNLVSLGFQVPKPDlISQLEQGEEP 59
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 1-29 5.90e-13

KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.


Pssm-ID: 460171  Cd Length: 42  Bit Score: 62.87  E-value: 5.90e-13
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1609559042   1 MDFTPEEWGKLDPAQR----DVMLENYRNLVSL 29
Cdd:pfam01352   9 VDFTQEEWALLDPAQRnlyrDVMLENYRNLVSL 41
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 1-29 1.59e-11

KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta , KRAB-A interacting protein , and tripartite motif protein 28). The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation.


Pssm-ID: 143639  Cd Length: 40  Bit Score: 58.72  E-value: 1.59e-11
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1609559042   1 MDFTPEEWGKLDPAQR----DVMLENYRNLVSL 29
Cdd:cd07765     8 VYFSQEEWELLDPAQRdlyrDVMLENYENLVSL 40
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
301-456 2.49e-07

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 52.78  E-value: 2.49e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559042 301 KPYECNECDKAFIHSSALIKHQRT--HTGE--KPYKC--QECGKAFSHCSSLTKHQRVHTGEKPYEC--SECGKTFSQST 372
Cdd:COG5048   288 LPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEklLNSSSKFSPLL 367

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559042 373 H-----LVQHQRIHTGEKPYEC--NECGKTFSRSSNFAKHQRIHIGKKP--YKCSECGKAFIHSSALIQHQRTHTGEKPF 443
Cdd:COG5048   368 NneppqSLQQYKDLKNDKKSETlsNSCIRNFKRDSNLSLHIITHLSFRPynCKNPPCSKSFNRHYNLIPHKKIHTNHAPL 447

                         170
                  ....*....|...
gi 1609559042 444 RCNECGKSFKCSS 456
Cdd:COG5048   448 LCSILKSFRRDLD 460
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
171-310 2.56e-05

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 46.61  E-value: 2.56e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559042 171 KSLKQKSNLMKKQR----TYKEKKPHKC--NDCGELFTYHSVLIRHQRVHTGEKPYTC--NECGKSFS------HRANLT 236
Cdd:COG5048   297 ISFSRSSPLTRHLRsvnhSGESLKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEklLNSSSKFSpllnnePPQSLQ 376

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1609559042 237 KHQRTHTRILFEC--SECKKTFTESSSLATHQRIHVGERPYECN--ECGKGFNRSTHLVQHQLIHTGVKPYECNECDK 310
Cdd:COG5048   377 QYKDLKNDKKSETlsNSCIRNFKRDSNLSLHIITHLSFRPYNCKnpPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKS 454
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 413-467 6.15e-05

N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins; Oryza sativa SUPPRESSOR OF FRI 4 (OsSUF4) is a C2H2-type zinc finger transcription factor which interacts with the major H3K36 methyltransferase SDG725 to promote H3K36me3 (tri-methylation at H3K9) establishment. The transcription factor OsSUF4 recognizes a specific 7-bp DNA element (5'-CGGAAAT-3'), which is contained in the promoter regions of many genes throughout the rice genome. Through interaction with OsSUF4, SDG725 is recruited to the promoters of key florigen genes, RICE FLOWERING LOCUS T1 (RFT1) and Heading date 3a (Hd3a), for H3K36 deposition to promote gene activation and rice plant flowering. OsSUF4 target genes include a number of genes involved in many biological processes. Flowering plant Arabidopsis SUF4 binds to a 15bp DNA element (5'-CCAAATTTTAAGTTT-3') within the promoter of the floral repressor gene FLOWERING LOCUS C (FLC) and recruits the FRI-C transcription activator complex to the FLC promoter. Although the DNA-binding element and target genes of AtSUF4 are different from those of OsSUF4, AtSUF4 is known to interact with the Arabidopsis H3K36 methyltransferase SDG8 (also known as ASHH2/EFS/SET8), and the methylation deposition mechanism mediated by the SUF4 transcription factor and H3K36 methyltransferase may be conserved in Arabidopsis and rice. Proteins in this family have two conserved C2H2-type zinc finger motifs at the N-terminus (included in this model), and a large proline-rich domain at the C-terminus; for OsSUF4, it has been shown that the N-terminal zinc-finger domain is responsible for DNA binding, and that the C-terminal domain interacts with SDG725.


Pssm-ID: 411020 [Multi-domain]  Cd Length: 82  Bit Score: 41.39  E-value: 6.15e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1609559042 413 KPYkCSECGKAFIHSSALIQHQRTHTgekpFRCNECGKSFKCSSSLIRH-QRVHTE 467
Cdd:cd20908     1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHcLQVHKE 51
zf-H2C2_2 pfam13465
Zinc-finger double domain;
429-454 1.12e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 39.28  E-value: 1.12e-04
                          10        20
                  ....*....|....*....|....*.
gi 1609559042 429 ALIQHQRTHTGEKPFRCNECGKSFKC 454
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 220-242 3.55e-04

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 37.66  E-value: 3.55e-04
                          10        20
                  ....*....|....*....|...
gi 1609559042 220 YTCNECGKSFSHRANLTKHQRTH 242
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
 
Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
1-47 7.25e-18

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 77.25  E-value: 7.25e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1609559042    1 MDFTPEEWGKLDPAQ----RDVMLENYRNLVSLWLPVSKPE-SYNLENGKEP 47
Cdd:smart00349   8 VYFTQEEWEQLDPAQknlyRDVMLENYSNLVSLGFQVPKPDlISQLEQGEEP 59
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 1-29 5.90e-13

KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.


Pssm-ID: 460171  Cd Length: 42  Bit Score: 62.87  E-value: 5.90e-13
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1609559042   1 MDFTPEEWGKLDPAQR----DVMLENYRNLVSL 29
Cdd:pfam01352   9 VDFTQEEWALLDPAQRnlyrDVMLENYRNLVSL 41
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 1-29 1.59e-11

KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta , KRAB-A interacting protein , and tripartite motif protein 28). The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation.


Pssm-ID: 143639  Cd Length: 40  Bit Score: 58.72  E-value: 1.59e-11
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1609559042   1 MDFTPEEWGKLDPAQR----DVMLENYRNLVSL 29
Cdd:cd07765     8 VYFSQEEWELLDPAQRdlyrDVMLENYENLVSL 40
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
301-456 2.49e-07

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 52.78  E-value: 2.49e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559042 301 KPYECNECDKAFIHSSALIKHQRT--HTGE--KPYKC--QECGKAFSHCSSLTKHQRVHTGEKPYEC--SECGKTFSQST 372
Cdd:COG5048   288 LPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEklLNSSSKFSPLL 367

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559042 373 H-----LVQHQRIHTGEKPYEC--NECGKTFSRSSNFAKHQRIHIGKKP--YKCSECGKAFIHSSALIQHQRTHTGEKPF 443
Cdd:COG5048   368 NneppqSLQQYKDLKNDKKSETlsNSCIRNFKRDSNLSLHIITHLSFRPynCKNPPCSKSFNRHYNLIPHKKIHTNHAPL 447

                         170
                  ....*....|...
gi 1609559042 444 RCNECGKSFKCSS 456
Cdd:COG5048   448 LCSILKSFRRDLD 460
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
171-310 2.56e-05

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 46.61  E-value: 2.56e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559042 171 KSLKQKSNLMKKQR----TYKEKKPHKC--NDCGELFTYHSVLIRHQRVHTGEKPYTC--NECGKSFS------HRANLT 236
Cdd:COG5048   297 ISFSRSSPLTRHLRsvnhSGESLKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEklLNSSSKFSpllnnePPQSLQ 376

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1609559042 237 KHQRTHTRILFEC--SECKKTFTESSSLATHQRIHVGERPYECN--ECGKGFNRSTHLVQHQLIHTGVKPYECNECDK 310
Cdd:COG5048   377 QYKDLKNDKKSETlsNSCIRNFKRDSNLSLHIITHLSFRPYNCKnpPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKS 454
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 413-467 6.15e-05

N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins; Oryza sativa SUPPRESSOR OF FRI 4 (OsSUF4) is a C2H2-type zinc finger transcription factor which interacts with the major H3K36 methyltransferase SDG725 to promote H3K36me3 (tri-methylation at H3K9) establishment. The transcription factor OsSUF4 recognizes a specific 7-bp DNA element (5'-CGGAAAT-3'), which is contained in the promoter regions of many genes throughout the rice genome. Through interaction with OsSUF4, SDG725 is recruited to the promoters of key florigen genes, RICE FLOWERING LOCUS T1 (RFT1) and Heading date 3a (Hd3a), for H3K36 deposition to promote gene activation and rice plant flowering. OsSUF4 target genes include a number of genes involved in many biological processes. Flowering plant Arabidopsis SUF4 binds to a 15bp DNA element (5'-CCAAATTTTAAGTTT-3') within the promoter of the floral repressor gene FLOWERING LOCUS C (FLC) and recruits the FRI-C transcription activator complex to the FLC promoter. Although the DNA-binding element and target genes of AtSUF4 are different from those of OsSUF4, AtSUF4 is known to interact with the Arabidopsis H3K36 methyltransferase SDG8 (also known as ASHH2/EFS/SET8), and the methylation deposition mechanism mediated by the SUF4 transcription factor and H3K36 methyltransferase may be conserved in Arabidopsis and rice. Proteins in this family have two conserved C2H2-type zinc finger motifs at the N-terminus (included in this model), and a large proline-rich domain at the C-terminus; for OsSUF4, it has been shown that the N-terminal zinc-finger domain is responsible for DNA binding, and that the C-terminal domain interacts with SDG725.


Pssm-ID: 411020 [Multi-domain]  Cd Length: 82  Bit Score: 41.39  E-value: 6.15e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1609559042 413 KPYkCSECGKAFIHSSALIQHQRTHTgekpFRCNECGKSFKCSSSLIRH-QRVHTE 467
Cdd:cd20908     1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHcLQVHKE 51
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 301-353 6.52e-05

N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins; Oryza sativa SUPPRESSOR OF FRI 4 (OsSUF4) is a C2H2-type zinc finger transcription factor which interacts with the major H3K36 methyltransferase SDG725 to promote H3K36me3 (tri-methylation at H3K9) establishment. The transcription factor OsSUF4 recognizes a specific 7-bp DNA element (5'-CGGAAAT-3'), which is contained in the promoter regions of many genes throughout the rice genome. Through interaction with OsSUF4, SDG725 is recruited to the promoters of key florigen genes, RICE FLOWERING LOCUS T1 (RFT1) and Heading date 3a (Hd3a), for H3K36 deposition to promote gene activation and rice plant flowering. OsSUF4 target genes include a number of genes involved in many biological processes. Flowering plant Arabidopsis SUF4 binds to a 15bp DNA element (5'-CCAAATTTTAAGTTT-3') within the promoter of the floral repressor gene FLOWERING LOCUS C (FLC) and recruits the FRI-C transcription activator complex to the FLC promoter. Although the DNA-binding element and target genes of AtSUF4 are different from those of OsSUF4, AtSUF4 is known to interact with the Arabidopsis H3K36 methyltransferase SDG8 (also known as ASHH2/EFS/SET8), and the methylation deposition mechanism mediated by the SUF4 transcription factor and H3K36 methyltransferase may be conserved in Arabidopsis and rice. Proteins in this family have two conserved C2H2-type zinc finger motifs at the N-terminus (included in this model), and a large proline-rich domain at the C-terminus; for OsSUF4, it has been shown that the N-terminal zinc-finger domain is responsible for DNA binding, and that the C-terminal domain interacts with SDG725.


Pssm-ID: 411020 [Multi-domain]  Cd Length: 82  Bit Score: 41.39  E-value: 6.52e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1609559042 301 KPYeCNECDKAFIHSSALIKHQRTHTgekpYKCQECGKAFSHCSSLTKH-QRVH 353
Cdd:cd20908     1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHcLQVH 49
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
329-470 9.38e-05

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 44.69  E-value: 9.38e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559042 329 KPYKCQECGKAFSHCSSLTKHQR--VHTGE--KPYECSE--CGKTFSQSTHLVQHQRIHTGEKPYEC--NECGKTFSRSS 400
Cdd:COG5048   288 LPIKSKQCNISFSRSSPLTRHLRsvNHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSISPAKEklLNSSSKFSPLL 367

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1609559042 401 NFAKHQRI--HIGKKPYKCSE-----CGKAFIHSSALIQHQRTHTGEKP--FRCNECGKSFKCSSSLIRHQRVHTEEQP 470
Cdd:COG5048   368 NNEPPQSLqqYKDLKNDKKSEtlsnsCIRNFKRDSNLSLHIITHLSFRPynCKNPPCSKSFNRHYNLIPHKKIHTNHAP 446
zf-H2C2_2 pfam13465
Zinc-finger double domain;
429-454 1.12e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 39.28  E-value: 1.12e-04
                          10        20
                  ....*....|....*....|....*.
gi 1609559042 429 ALIQHQRTHTGEKPFRCNECGKSFKC 454
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
373-398 1.34e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.89  E-value: 1.34e-04
                          10        20
                  ....*....|....*....|....*.
gi 1609559042 373 HLVQHQRIHTGEKPYECNECGKTFSR 398
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
317-342 1.38e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.89  E-value: 1.38e-04
                          10        20
                  ....*....|....*....|....*.
gi 1609559042 317 ALIKHQRTHTGEKPYKCQECGKAFSH 342
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
357-409 3.52e-04

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 42.76  E-value: 3.52e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1609559042 357 KPYECSECGKTFSQSTHLVQHQRIHTGEKPYECN--ECGKTFSRSSNFAKHQRIH 409
Cdd:COG5048    32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSysGCDKSFSRPLELSRHLRTH 86
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 220-242 3.55e-04

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 37.66  E-value: 3.55e-04
                          10        20
                  ....*....|....*....|...
gi 1609559042 220 YTCNECGKSFSHRANLTKHQRTH 242
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-H2C2_2 pfam13465
Zinc-finger double domain;
207-231 3.92e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 37.74  E-value: 3.92e-04
                          10        20
                  ....*....|....*....|....*
gi 1609559042 207 LIRHQRVHTGEKPYTCNECGKSFSH 231
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSFKS 26
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 357-409 4.49e-04

N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins; Oryza sativa SUPPRESSOR OF FRI 4 (OsSUF4) is a C2H2-type zinc finger transcription factor which interacts with the major H3K36 methyltransferase SDG725 to promote H3K36me3 (tri-methylation at H3K9) establishment. The transcription factor OsSUF4 recognizes a specific 7-bp DNA element (5'-CGGAAAT-3'), which is contained in the promoter regions of many genes throughout the rice genome. Through interaction with OsSUF4, SDG725 is recruited to the promoters of key florigen genes, RICE FLOWERING LOCUS T1 (RFT1) and Heading date 3a (Hd3a), for H3K36 deposition to promote gene activation and rice plant flowering. OsSUF4 target genes include a number of genes involved in many biological processes. Flowering plant Arabidopsis SUF4 binds to a 15bp DNA element (5'-CCAAATTTTAAGTTT-3') within the promoter of the floral repressor gene FLOWERING LOCUS C (FLC) and recruits the FRI-C transcription activator complex to the FLC promoter. Although the DNA-binding element and target genes of AtSUF4 are different from those of OsSUF4, AtSUF4 is known to interact with the Arabidopsis H3K36 methyltransferase SDG8 (also known as ASHH2/EFS/SET8), and the methylation deposition mechanism mediated by the SUF4 transcription factor and H3K36 methyltransferase may be conserved in Arabidopsis and rice. Proteins in this family have two conserved C2H2-type zinc finger motifs at the N-terminus (included in this model), and a large proline-rich domain at the C-terminus; for OsSUF4, it has been shown that the N-terminal zinc-finger domain is responsible for DNA binding, and that the C-terminal domain interacts with SDG725.


Pssm-ID: 411020 [Multi-domain]  Cd Length: 82  Bit Score: 39.08  E-value: 4.49e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1609559042 357 KPYeCSECGKTFSQSTHLVQHQRIHTgekpYECNECGKTFSRSSNFAKH-QRIH 409
Cdd:cd20908     1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHcLQVH 49
zf-H2C2_2 pfam13465
Zinc-finger double domain;
345-370 6.27e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 36.97  E-value: 6.27e-04
                          10        20
                  ....*....|....*....|....*.
gi 1609559042 345 SLTKHQRVHTGEKPYECSECGKTFSQ 370
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
186-463 6.42e-04

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 41.99  E-value: 6.42e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559042 186 YKEKKPHKCNDCGELFTYHSVLIRHQRVHTGEKPYTCN--ECGKSFSHRANLTKHQRTHTrilfecseckkTFTESSSLA 263
Cdd:COG5048    28 SNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSysGCDKSFSRPLELSRHLRTHH-----------NNPSDLNSK 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559042 264 THQRIHVGERPYECNECGKGFNRSTHLVQH---------QLIHTGVKPYECNECDKAFIHSSALIKhQRTHTgEKPYKCQ 334
Cdd:COG5048    97 SLPLSNSKASSSSLSSSSSNSNDNNLLSSHslppssrdpQLPDLLSISNLRNNPLPGNNSSSVNTP-QSNSL-HPPLPAN 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559042 335 ECGKAFSHCSSLTKHQRVHTGEKPYECSECGKTFSQSTHLVQHQRIHTGEKPYECNECGKTFSRSSNFAKHQRIhigKKP 414
Cdd:COG5048   175 SLSKDPSSNLSLLISSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSL---SSS 251

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1609559042 415 YKCSECGKAFIHSSALIQHQRTH----------TGEKPFRCNECGKSFKCSSSLIRHQR 463
Cdd:COG5048   252 DSSSSASESPRSSLPTASSQSSSpnesdsssekGFSLPIKSKQCNISFSRSSPLTRHLR 310
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 387-409 9.36e-04

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 36.51  E-value: 9.36e-04
                          10        20
                  ....*....|....*....|...
gi 1609559042 387 YECNECGKTFSRSSNFAKHQRIH 409
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-H2C2_2 pfam13465
Zinc-finger double domain;
401-426 1.40e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 36.20  E-value: 1.40e-03
                          10        20
                  ....*....|....*....|....*.
gi 1609559042 401 NFAKHQRIHIGKKPYKCSECGKAFIH 426
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
289-314 1.79e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 35.81  E-value: 1.79e-03
                          10        20
                  ....*....|....*....|....*.
gi 1609559042 289 HLVQHQLIHTGVKPYECNECDKAFIH 314
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 331-353 2.18e-03

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 35.35  E-value: 2.18e-03
                          10        20
                  ....*....|....*....|...
gi 1609559042 331 YKCQECGKAFSHCSSLTKHQRVH 353
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 415-437 3.42e-03

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 34.97  E-value: 3.42e-03
                          10        20
                  ....*....|....*....|...
gi 1609559042 415 YKCSECGKAFIHSSALIQHQRTH 437
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 303-325 3.55e-03

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 34.97  E-value: 3.55e-03
                          10        20
                  ....*....|....*....|...
gi 1609559042 303 YECNECDKAFIHSSALIKHQRTH 325
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 359-381 4.91e-03

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 34.58  E-value: 4.91e-03
                          10        20
                  ....*....|....*....|...
gi 1609559042 359 YECSECGKTFSQSTHLVQHQRIH 381
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
385-465 5.13e-03

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 39.29  E-value: 5.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559042 385 KPYECNECGKTFSRSSNFAKHQRIHIGKKPYKCS--ECGKAFIHSSALIQHQRTHTGEKPFRCNECGKS--FKCSSSLIR 460
Cdd:COG5048    32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSysGCDKSFSRPLELSRHLRTHHNNPSDLNSKSLPLsnSKASSSSLS 111


                  ....*
gi 1609559042 461 HQRVH 465
Cdd:COG5048   112 SSSSN 116
zf-H2C2_2 pfam13465
Zinc-finger double domain;
261-286 8.23e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 33.88  E-value: 8.23e-03
                          10        20
                  ....*....|....*....|....*.
gi 1609559042 261 SLATHQRIHVGERPYECNECGKGFNR 286
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
SFP1 COG5189
Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division ...
 383-466 9.38e-03

Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning];


Pssm-ID: 227516 [Multi-domain]  Cd Length: 423  Bit Score: 38.16  E-value: 9.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559042 383 GEKPYECN--ECGKTFsRSSNFAKHQRIHigkkpykcSECGKAFIHSSALIQHQRTHTGEKPFRCNECGKSFKCSSSLIR 460
Cdd:COG5189   346 DGKPYKCPveGCNKKY-KNQNGLKYHMLH--------GHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKY 416


                  ....*.
gi 1609559042 461 HqRVHT 466
Cdd:COG5189   417 H-RKHS 421
 
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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