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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26328291 238 PSKPEKAPGSGKPYECNHCGKVLSHKQGLLDHQRTHTGEKPYECNECGIAFSQK--SHLVVHQRTHTGEKPYECEQCGKA 315
Cdd:COG5048  21 KSTLKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSrpLELSRHLRTHHNNPSDLNSKSLPL 100

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26328291 316 HGHKHALTDHLRIHTGE-KPYKCNECGKTFRHSSNLMQHLRSHTGEKPYECKECGKSFR----YNSSLTEHVRTHTGEIP 390
Cdd:COG5048 101 SNSKASSSSLSSSSSNSnDNNLLSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSSVntpqSNSLHPPLPANSLSKDP 180

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26328291 391 YECNecgkafkygsSLTKHMRIHTGEKPFECNECGKTFSKKSHLVIHQRTHTKEKPYKCDECGKAFGHSSSLTYHMRTHT 470
Cdd:COG5048 181 SSNL----------SLLISSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSS 250

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26328291 471 GDCPFECNQCGKAFKQIEGLTQHQRVHTGE-------KPYECVECGKAFSQKSHLIVHQRT--HTGE--KPFECYE--CG 537
Cdd:COG5048 251 SDSSSSASESPRSSLPTASSQSSSPNESDSssekgfsLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPYslCG 330

                       330       340
                ....*....|....*....|....*
gi 26328291 538 KAFNAKSQLVIHQRSHTGEKPYECI 562
Cdd:COG5048 331 KLFSRNDALKRHILLHTSISPAKEK 355

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 26328291   1 MATSEPAEsdaEWEQLEPVQRDVYKDTKLENCSNPASM 38
Cdd:cd07765   6 VAVYFSQE---EWELLDPAQRDLYRDVMLENYENLVSL 40

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
                  ....*....|....*....|....*...
gi 26328291    12 EWEQLEPVQRDVYKDTKLENCSNPASMG 39
Cdd:pfam01352  15 EWALLDPAQRNLYRDVMLENYRNLVSLG 42

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 26328291 417 KPFeCNECGKTFSKKSHLVIHQRTHTkekpYKCDECGKAFGHSSSLTYHMRT 468
Cdd:cd20908   1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHCLQ 47

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 26328291   1 MATSEPAEsdaEWEQLEPVQRDVYKDTKLENCSNPASM 38
Cdd:cd07765   6 VAVYFSQE---EWELLDPAQRDLYRDVMLENYENLVSL 40

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26328291 120 YGLLENKSLHSKHTPSEKKLLKSSSRGENSNQNSDslkkKPDTANDHRKSLSHSASDVNKDEIPTRKKCDKLPNNKLSDK 199
Cdd:COG5048  74 SRPLELSRHLRTHHNNPSDLNSKSLPLSNSKASSS----SLSSSSSNSNDNNLLSSHSLPPSSRDPQLPDLLSISNLRNN 149

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26328291 200 GDKNQTSKKCEKVCRHSASHTKEDKIQTgeKRKSHCRTPSKPEKAPGSGKPYECNHCGKVLSHKQGLLDHQRTHTGEKPY 279
Cdd:COG5048 150 PLPGNNSSSVNTPQSNSLHPPLPANSLS--KDPSSNLSLLISSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSL 227

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26328291 280 ECNECGIAF------SQKSHLVVHQRTHTGEKPYECEQCGKAHGHKHALTDHLRIHTG-EKPYKCNECGKTFRHSSNLMQ 352
Cdd:COG5048 228 PLTTNSQLSpksllsQSPSSLSSSDSSSSASESPRSSLPTASSQSSSPNESDSSSEKGfSLPIKSKQCNISFSRSSPLTR 307

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26328291 353 HLRS--HTGE--KPYECKE--CGKSFRYNSSLTEHVRTHTGEIPYECNECGKAFKYGSSLTK-------HMRIHTGEKPF 419
Cdd:COG5048 308 HLRSvnHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNeppqslqQYKDLKNDKKS 387

                       330       340       350       360       370       380
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 26328291 420 EC--NECGKTFSKKSHLVIHQRTHTKEKP--YKCDECGKAFGHSSSLTYHMRTHTGDCPFECNQCGK 482
Cdd:COG5048 388 ETlsNSCIRNFKRDSNLSLHIITHLSFRPynCKNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKS 454

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26328291 325 HLRIHTGEKPYKCNECGKTFRHSSNLMQHLRSHTGEKPYECKECGKSF------RYNSSLTEHVRTHTGEIPYECNECGK 398
Cdd:COG5048 189 SSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSpksllsQSPSSLSSSDSSSSASESPRSSLPTA 268

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26328291 399 AFKYGSSLTKHMRIHTG-EKPFECNECGKTFSKKSHLVIHQRT--HTKE--KPYKCDE--CGKAFGHSSSLTYHMRTHTG 471
Cdd:COG5048 269 SSQSSSPNESDSSSEKGfSLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTS 348

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26328291 472 DCPFEC--NQCGKAFKQI-----EGLTQHQRVHTGEKPYECV--ECGKAFSQKSHLIVHQRTHTGEKPFECY--ECGKAF 540
Cdd:COG5048 349 ISPAKEklLNSSSKFSPLlnnepPQSLQQYKDLKNDKKSETLsnSCIRNFKRDSNLSLHIITHLSFRPYNCKnpPCSKSF 428

                       250       260       270
                ....*....|....*....|....*....|.
gi 26328291 541 NAKSQLVIHQRSHTGEKPYECIECGKAFKQN 571
Cdd:COG5048 429 NRHYNLIPHKKIHTNHAPLLCSILKSFRRDL 459

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26328291 125 NKSLHSKHTPSEKKLLKSSSRGENSNQNSDSLKKKPDTANDHRKSLSHSASDVNKDEIPTRKKCDK-------LPNNKLS 197
Cdd:COG5048  98 LPLSNSKASSSSLSSSSSNSNDNNLLSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSSVNTPQsnslhppLPANSLS 177

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26328291 198 DKGDKNQTSKKCEKVcRHSASHTKEDKIQTGEKRKSHCRTPSKPEKAPGSGKPYECNHCGK---VLSHKQGLLDHQRTHT 274
Cdd:COG5048 178 KDPSSNLSLLISSNV-STSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPkslLSQSPSSLSSSDSSSS 256

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26328291 275 GEKPYECNECGIAFSQKSHLVVHQRTHTG-EKPYECEQCGKAHGHKHALTDHLR--IHTGE--KPYKCNE--CGKTFRHS 347
Cdd:COG5048 257 ASESPRSSLPTASSQSSSPNESDSSSEKGfSLPIKSKQCNISFSRSSPLTRHLRsvNHSGEslKPFSCPYslCGKLFSRN 336

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26328291 348 SNLMQHLRSHTGEKPYECKECGKSFRYNSSLTE-------HVRTHTGEIPYEC--NECGKAFKYGSSLTKHMRIHTGEKP 418
Cdd:COG5048 337 DALKRHILLHTSISPAKEKLLNSSSKFSPLLNNeppqslqQYKDLKNDKKSETlsNSCIRNFKRDSNLSLHIITHLSFRP 416

                       330       340       350       360
                ....*....|....*....|....*....|....*....|.
gi 26328291 419 --FECNECGKTFSKKSHLVIHQRTHTKEKPYKCDECGKAFG 457
Cdd:COG5048 417 ynCKNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKSFRR 457

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*.
gi 26328291   321 ALTDHLRIHTGEKPYKCNECGKTFRH 346
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*
gi 26328291   546 LVIHQRSHTGEKPYECIECGKAFKQ 570
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSFKS 26

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....
gi 26328291   433 HLVIHQRTHTKEKPYKCDECGKAF 456
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 26328291 417 KPFeCNECGKTFSKKSHLVIHQRTHTkekpYKCDECGKAFGHSSSLTYHMRT 468
Cdd:cd20908   1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHCLQ 47

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 26328291   503 YECVECGKAFSQKSHLIVHQRTH 525
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 26328291   363 YECKECGKSFRYNSSLTEHVRTH 385
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|...
gi 26328291   293 HLVVHQRTHTGEKPYECEQCGKA 315
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKS 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 26328291   279 YECNECGIAFSQKSHLVVHQRTH 301
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 26328291 501 KPYeCVECGKAFSQKSHLIVHQRTHTgekpFECYECGKAFNAKSQLVIH 549
Cdd:cd20908   1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVH 44