krueppel associated box;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 296010923    27 VTFEDVAVDFTQEEWQYLNPPQRTLYRDVMLETYSNLVFVGQQVTKPNLILKLEVEECP 85
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEP 59

krueppel associated box;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 296010923    27 VTFEDVAVDFTQEEWQYLNPPQRTLYRDVMLETYSNLVFVGQQVTKPNLILKLEVEECP 85
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEP 59

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 296010923  27 VTFEDVAVDFTQEEWQYLNPPQRTLYRDVMLETYSNLVF 65
Cdd:cd07765    1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVS 39

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 296010923 376 CNECKKTFSDKSTLIIHQRTHtgekpH-KCTECGKSFNEKSTLIVH 420
Cdd:cd20908    4 CYYCDREFDDEKILIQHQKAK-----HfKCHICHKKLYTAGGLAVH 44

krueppel associated box;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 296010923    27 VTFEDVAVDFTQEEWQYLNPPQRTLYRDVMLETYSNLVFVGQQVTKPNLILKLEVEECP 85
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEP 59

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 296010923  27 VTFEDVAVDFTQEEWQYLNPPQRTLYRDVMLETYSNLVF 65
Cdd:cd07765    1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVS 39

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296010923 147 STNLVASIQRPDKHESFGNNMvdnldlfsrssaENKYDNGCAKLFFHTEYEK----TNPGMKPYGYKECGKGLRRKKGLS 222
Cdd:COG5048   11 SNNSVLSSTPKSTLKSLSNAP------------RPDSCPNCTDSFSRLEHLTrhirSHTGEKPSQCSYSGCDKSFSRPLE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296010923 223 L--HQRIKNGEKPFECTACR-KTFSKKSHLIVHWRTHTGEKPFGCTECGKAFSQKSQLIIHLRTHTGERPFECPECGKAF 299
Cdd:COG5048   79 LsrHLRTHHNNPSDLNSKSLpLSNSKASSSSLSSSSSNSNDNNLLSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSS 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296010923 300 RE----------------------KSTVIIHYRTHTGEKPYECNECGKAFTQKSNLIVHQKTHTGEKTYECTKCGESF-- 355
Cdd:COG5048  159 VNtpqsnslhpplpanslskdpssNLSLLISSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSpk 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296010923 356 ----IQKLDLIIHHSTHTGKKPHECNECKKTFSDKSTLIIHQRTHTG-EKPHKCTECGKSFNEKSTLIVHQRT--HTGE- 427
Cdd:COG5048  239 sllsQSPSSLSSSDSSSSASESPRSSLPTASSQSSSPNESDSSSEKGfSLPIKSKQCNISFSRSSPLTRHLRSvnHSGEs 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296010923 428 -KPYECDV--CGKTFTQKSNLGVHQRTHSGEKPFEC--NECEKAFSQKSY-----LMLHQRGHTGEKPYEC--NECEKAF 495
Cdd:COG5048  319 lKPFSCPYslCGKLFSRNDALKRHILLHTSISPAKEklLNSSSKFSPLLNneppqSLQQYKDLKNDKKSETlsNSCIRNF 398

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 296010923 496 SQKSYLIIHQRTHTEEKP--YKCNECGKAFREKSKLIIHQRIHTgEKPYECPVCWKAFSQ 553
Cdd:COG5048  399 KRDSNLSLHIITHLSFRPynCKNPPCSKSFNRHYNLIPHKKIHT-NHAPLLCSILKSFRR 457

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296010923 371 KKPHECNECKKTFSDKSTLIIHQRTHTGEKPHKCT--ECGKSFNEKSTLIVHQRTHTGEKPYECDVCGKtfTQKSNLGVH 448
Cdd:COG5048   31 PRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSysGCDKSFSRPLELSRHLRTHHNNPSDLNSKSLP--LSNSKASSS 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296010923 449 QRTHSGEKPFECN-ECEKAFSQKSYL----MLHQRGHTGEKPYE-CNECEKAFSQKSYLI-------------------I 503
Cdd:COG5048  109 SLSSSSSNSNDNNlLSSHSLPPSSRDpqlpDLLSISNLRNNPLPgNNSSSVNTPQSNSLHpplpanslskdpssnlsllI 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296010923 504 HQRTHTEEKPYKCNECGKAFREKSKLIIHQRIHTGEKPYECPVCWKAFSQKSQLIIHQRTHTGEKPYACTECGKAFREKS 583
Cdd:COG5048  189 SSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDSSSSASESPRSSLPTA 268

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 296010923 584 TFTVHQRTHTGE-------KPYKCTECGKAFTQKSNLIVHQRT 619
Cdd:COG5048  269 SSQSSSPNESDSssekgfsLPIKSKQCNISFSRSSPLTRHLRS 311

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|..
gi 296010923  588 HQRTHTGEKPYKCTECGKAFTQ 609
Cdd:pfam13465   5 HMRTHTGEKPYKCPECGKSFKS 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 296010923  598 YKCTECGKAFTQKSNLIVHQRTH 620
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        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 296010923 484 KPYeCNECEKAFSQKSYLIIHQRTHTeekpYKCNECGKAFREKSKLIIH-QRIH 536
Cdd:cd20908    1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHcLQVH 49

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*.
gi 296010923  472 YLMLHQRGHTGEKPYECNECEKAFSQ 497
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 296010923  318 YECNECGKAFTQKSNLIVHQKTH 340
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296010923 454 GEKPFECN--ECEKAFSQKSYLMLHQR-GHTGEKPYECNECEKafsqksyliiHQRTHTEEKPYKCNECGKAFREKSKLI 530
Cdd:COG5189  346 DGKPYKCPveGCNKKYKNQNGLKYHMLhGHQNQKLHENPSPEK----------MNIFSAKDKPYRCEVCDKRYKNLNGLK 415

                 ..
gi 296010923 531 IH 532
Cdd:COG5189  416 YH 417

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|
gi 296010923  560 HQRTHTGEKPYACTECGKAF 579
Cdd:pfam13465   5 HMRTHTGEKPYKCPECGKSF 24

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....
gi 296010923  500 YLIIHQRTHTEEKPYKCNECGKAF 523
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 296010923  374 HECNECKKTFSDKSTLIIHQRTH 396
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23

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 296010923  402 HKCTECGKSFNEKSTLIVHQRTH 424
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*.
gi 296010923  332 NLIVHQKTHTGEKTYECTKCGESFIQ 357
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26