krueppel associated box;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1244518123    2 SDDEWKRLVPVQRALYKAVMLENYESIISLGLPVPRPDVILQFKRRGEPWI 52
Cdd:smart00349  11 TQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEPWI 61

krueppel associated box;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1244518123    2 SDDEWKRLVPVQRALYKAVMLENYESIISLGLPVPRPDVILQFKRRGEPWI 52
Cdd:smart00349  11 TQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEPWI 61

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 1244518123   2 SDDEWKRLVPVQRALYKAVMLENYESIISL 31
Cdd:cd07765    11 SQEEWELLDPAQRDLYRDVMLENYENLVSL 40

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*.
gi 1244518123 161 SLIRHQRTHTGEKPYDCPECGKAFSH 186
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26

krueppel associated box;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1244518123    2 SDDEWKRLVPVQRALYKAVMLENYESIISLGLPVPRPDVILQFKRRGEPWI 52
Cdd:smart00349  11 TQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEPWI 61

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 1244518123   2 SDDEWKRLVPVQRALYKAVMLENYESIISL 31
Cdd:cd07765    11 SQEEWELLDPAQRDLYRDVMLENYENLVSL 40

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1244518123 160 SSLIRHQRTHTGEKPYDCPECGKAFSHRSSLSRHLMFHTGESPYECDACGKAFFDRSSLTVHQRIHTGE-------KPFK 232
Cdd:COG5048   212 PSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDSSSSASESPRSSLPTASSQSSSPNESDSssekgfsLPIK 291

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1244518123 233 CNDCGKAFFDRSSLTRHQR--IHTGES--PYEC--QQCGKAFSQKSILTRHLLTHTGRKPYEC--RDCGKAFYG------ 298
Cdd:COG5048   292 SKQCNISFSRSSPLTRHLRsvNHSGESlkPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEklLNSSSKFSPllnnep 371

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1244518123 299 VTSLNRHQKVHTEEPRYQCSECGKAFFDRSSLTQHQKI-HTGDKPYEC--GECGKAFSQRCRLTRHQRVHTGEKPFECSV 375
Cdd:COG5048   372 PQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIItHLSFRPYNCknPPCSKSFNRHYNLIPHKKIHTNHAPLLCSI 451

                  ...
gi 1244518123 376 CGK 378
Cdd:COG5048   452 LKS 454

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*.
gi 1244518123 161 SLIRHQRTHTGEKPYDCPECGKAFSH 186
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
                  ....*....|....*....|....*....|....*....|....*..
gi 1244518123 149 CSECGKTFFDHSSLIRHQRTHTgekpYDCPECGKAFSHRSSLSRHLM 195
Cdd:cd20908     4 CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHCL 46

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*.
gi 1244518123 329 SLTQHQKIHTGDKPYECGECGKAFSQ 354
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 1244518123 231 FKCNDCGKAFFDRSSLTRHQRIH 253
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....
gi 1244518123 189 SLSRHLMFHTGESPYECDACGKAF 212
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSF 24

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 1244518123 148 ECSECGKTFFDHSSLIRHQRTH 169
Cdd:pfam00096   2 KCPDCGKSFSRKSNLKRHLRTH 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 1244518123 208 CGKAFFDRSSLTVHQRIHTgekpFKCNDCGKAFFDRSSLTRH-QRIH 253
Cdd:cd20908     7 CDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHcLQVH 49