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
                  ....*....|....*....|....
gi 2462548381  16 VNLEDVAVYLSGEEPRCMDPAQRD 39
Cdd:cd07765     1 VTFEDVAVYFSQEEWELLDPAQRD 24

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
                  ....*....|....*....|....
gi 2462548381  16 VNLEDVAVYLSGEEPRCMDPAQRD 39
Cdd:cd07765     1 VTFEDVAVYFSQEEWELLDPAQRD 24

krueppel associated box;

                           10        20        30
                   ....*....|....*....|....*....|...
gi 2462548381   16 VNLEDVAVYLSGEEPRCMDPAQ----RDAPLEN 44
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQknlyRDVMLEN 33

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
                  ....*....|....*....|....*....|....*....|....*....
gi 2462548381 143 RPYkCLVCGKGFSDRSNFSTHQRvhtgEKPYPCPECGKRFSQSSSLVIH 191
Cdd:cd20908     1 KPW-CYYCDREFDDEKILIQHQK----AKHFKCHICHKKLYTAGGLAVH 44

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
                  ....*....|....*....|....
gi 2462548381  16 VNLEDVAVYLSGEEPRCMDPAQRD 39
Cdd:cd07765     1 VTFEDVAVYFSQEEWELLDPAQRD 24

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462548381 155 SDRSNFSTHQRvhtgekPYPCPECGKRFSQSSSLVIHRRTHSGERPYACTQ--CGKRFNNSSHFSAHRRTHTGEKPYTCP 232
Cdd:COG5048    22 STLKSLSNAPR------PDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYsgCDKSFSRPLELSRHLRTHHNNPSDLNS 95

                  ....
gi 2462548381 233 ACGR 236
Cdd:COG5048    96 KSLP 99

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462548381 143 RPYKCLVCGKGFSDRSNFSTHQRVHTGEKPYPC--PECGKRFSQSSSLVIHRRTHSGERPYACTQCGKRFNNSS 214
Cdd:COG5048    32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHHNNPSDLNSKSLPLSNSKA 105

krueppel associated box;

                           10        20        30
                   ....*....|....*....|....*....|...
gi 2462548381   16 VNLEDVAVYLSGEEPRCMDPAQ----RDAPLEN 44
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQknlyRDVMLEN 33

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*
gi 2462548381 131 HLTKHQRTHTGERPYKCLVCGKGFS 155
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFK 25

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462548381 199 RPYACTQCGKRFNNSSHFSAHRRTHTGEKPYTCPACGRGFRRGT--DLHKHQRTHMGAGSLPTLQPVAP 265
Cdd:COG5048    32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRplELSRHLRTHHNNPSDLNSKSLPL 100

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*.
gi 2462548381 187 SLVIHRRTHSGERPYACTQCGKRFNN 212
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26

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 2462548381 145 YKCLVCGKGFSDRSNFSTHQRVH 167
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23

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
                  ....*....|....*....|....*....|....*....|....*....
gi 2462548381 143 RPYkCLVCGKGFSDRSNFSTHQRvhtgEKPYPCPECGKRFSQSSSLVIH 191
Cdd:cd20908     1 KPW-CYYCDREFDDEKILIQHQK----AKHFKCHICHKKLYTAGGLAVH 44

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462548381 115 KPYTCP--ECGKGFsKTSHLTKHQRTHTGerpykclvCGKGFSDRSNFSTHQRVHTGEKPYPCPECGKRFSQSSSLVIHr 192
Cdd:COG5189   348 KPYKCPveGCNKKY-KNQNGLKYHMLHGH--------QNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYH- 417

                  ....
gi 2462548381 193 RTHS 196
Cdd:COG5189   418 RKHS 421

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462548381 141 GERPYKCLV--CGKGFSDRSNFSTHQRV-HTGEK--PYPCPECGKRFSQSsslvihrrthsgERPYACTQCGKRFNNSSH 215
Cdd:COG5189   346 DGKPYKCPVegCNKKYKNQNGLKYHMLHgHQNQKlhENPSPEKMNIFSAK------------DKPYRCEVCDKRYKNLNG 413

                  ....*....
gi 2462548381 216 FSAHrRTHT 224
Cdd:COG5189   414 LKYH-RKHS 421

zinc finger;

                           10        20
                   ....*....|....*....|...
gi 2462548381  173 YPCPECGKRFSQSSSLVIHRRTH 195
Cdd:smart00355   1 YRCPECGKVFKSKSALREHMRTH 23