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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 6677631      1 MVTFRDVAVVFSEEELGLLDAAQRKLYHDVMLENFRMLLSVG 42
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*
gi 6677631    423 YLKAHQRVHTGEKPYRCEECGKGFS 447
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFK 25

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 6677631      1 MVTFRDVAVVFSEEELGLLDAAQRKLYHDVMLENFRMLLSVG 42
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42

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.

                        10        20        30
                ....*....|....*....|....*....|....*....
gi 6677631    2 VTFRDVAVVFSEEELGLLDAAQRKLYHDVMLENFRMLLS 40
Cdd:cd07765   1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVS 39

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*.
gi 6677631    283 DLNVHCRIHTGEKPYKCETCGKAFSR 308
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 6677631  239 KPYvCEECGKGFSQASHLLAHQRGHTgekpYKCSTCGKGFSRSSDLNVHC 288
Cdd:cd20908   1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHC 45

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*
gi 6677631    172 LQAHQVRHTGEKPYKCEECGKGFTR 196
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSFKS 26

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 6677631      1 MVTFRDVAVVFSEEELGLLDAAQRKLYHDVMLENFRMLLSVG 42
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42

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.

                        10        20        30
                ....*....|....*....|....*....|....*....
gi 6677631    2 VTFRDVAVVFSEEELGLLDAAQRKLYHDVMLENFRMLLS 40
Cdd:cd07765   1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVS 39

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6677631  157 YRCEKCDHAFCRLSGLQAHQVRHTGEKPYKC--EECGKGFTRASTLLDHQRGHTGNKPY----QCHACWKSFCHSSEFNN 230
Cdd:COG5048  34 DSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHHNNPSDlnskSLPLSNSKASSSSLSSS 113

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6677631  231 HirvHTGEKPYVCEECGKGFSQA----------SHLL--AHQRGHTGEKPYKCSTC----------GKGFSRSSDLNVHC 288
Cdd:COG5048 114 S---SNSNDNNLLSSHSLPPSSRdpqlpdllsiSNLRnnPLPGNNSSSVNTPQSNSlhpplpanslSKDPSSNLSLLISS 190

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6677631  289 RIHTGEKPYKCETCGKAFSRVSILQVHQRVHSEDKPYQCAECGRGF----TVESHLQAHQRSHTGERPYQCEECG--RGF 362
Cdd:COG5048 191 NVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSpkslLSQSPSSLSSSDSSSSASESPRSSLptASS 270

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6677631  363 CRASNFLAHRGVHTG-EKPYRCDICGKRFRQRSYLHDH--HRIHTGE--KPYKCEE--CGKVFSWSSYLKAHQRVHTGEK 435
Cdd:COG5048 271 QSSSPNESDSSSEKGfSLPIKSKQCNISFSRSSPLTRHlrSVNHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSIS 350

                ....
gi 6677631  436 PYRC 439
Cdd:COG5048 351 PAKE 354

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6677631  166 FCRLSGLQAHQVRHTG-EKPYKCEECGKGFTRASTLLDHQRG--HTG--NKPYQC--HACWKSFCHSSEFNNHIRVHTGE 238
Cdd:COG5048 270 SQSSSPNESDSSSEKGfSLPIKSKQCNISFSRSSPLTRHLRSvnHSGesLKPFSCpySLCGKLFSRNDALKRHILLHTSI 349

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6677631  239 KPYVC--EECGKGFSQASHLLAHQR-----GHTGEKPY------KCSTCGKGFSRSSDLNVHCRihTGEKPYKCETCGKA 305
Cdd:COG5048 350 SPAKEklLNSSSKFSPLLNNEPPQSlqqykDLKNDKKSetlsnsCIRNFKRDSNLSLHIITHLS--FRPYNCKNPPCSKS 427

                       170       180
                ....*....|....*....|....*..
gi 6677631  306 FSRVSILQVHQRVHSEDKPYQCAECGR 332
Cdd:COG5048 428 FNRHYNLIPHKKIHTNHAPLLCSILKS 454

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6677631  267 KPYKCSTCGKGFSRSSDLNVHCRIHTGEKPYKC--ETCGKAFSRVSILQVHQRVHSEDKPYQCA 328
Cdd:COG5048  32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHHNNPSDLNS 95

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6677631  379 KPYRCDICGKRFRQRSYLHDHHRIHTGEKPYKC--EECGKVFSWSSYLKAHQRVHTGEKPYRCE 440
Cdd:COG5048  32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHHNNPSDLNS 95

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 6677631  239 KPYvCEECGKGFSQASHLLAHQRGHTgekpYKCSTCGKGFSRSSDLNVHC 288
Cdd:cd20908   1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHC 45

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*
gi 6677631    172 LQAHQVRHTGEKPYKCEECGKGFTR 196
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSFKS 26

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....
gi 6677631    339 HLQAHQRSHTGERPYQCEECGRGF 362
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSF 24

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 6677631  323 KPYqCAECGRGFTVESHLQAHQRSHTgerpYQCEECGRGFCRASNFLAH-RGVH 375
Cdd:cd20908   1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHcLQVH 49

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.

                          10        20
                  ....*....|....*....|...
gi 6677631    381 YRCDICGKRFRQRSYLHDHHRIH 403
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23