leucine rich region;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016470381   48 PETFRQQFRQFGYQDSPGPHEALSRLWELCHLWLRPEVHTKEQILELLVLEQFLAILPKELQAWVQKHHPENGEETVTML 127
Cdd:smart00431   1 PEIFRQRFRQFRYQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLL 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1016470381  128 EDVERELDGPKQIFFG--RRKDMIAEKLAPSE 157
Cdd:smart00431  81 EDLERELDEPGQQVSAhvHGQEVLLEKMVPLG 112

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 1016470381 307 YKCHDCGKAFSQSSNLFRHRKRH 329
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23

leucine rich region;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016470381   48 PETFRQQFRQFGYQDSPGPHEALSRLWELCHLWLRPEVHTKEQILELLVLEQFLAILPKELQAWVQKHHPENGEETVTML 127
Cdd:smart00431   1 PEIFRQRFRQFRYQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLL 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1016470381  128 EDVERELDGPKQIFFG--RRKDMIAEKLAPSE 157
Cdd:smart00431  81 EDLERELDEPGQQVSAhvHGQEVLLEKMVPLG 112

SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several vertebrate proteins that contain C2H2 zinc finger motifs, many of which may be transcription factors playing roles in cell survival and differentiation. This protein-interaction domain is able to mediate homo- and hetero-oligomerization of SCAN-containing proteins. Some SCAN-containing proteins, including those of lower vertebrates, do not contain zinc finger motifs. It has been noted that the SCAN domain resembles a domain-swapped version of the C-terminal domain of the HIV capsid protein. This domain model features elements common to the three general groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B). The SCAND1 protein is truncated at the C-terminus with respect to this model, the SCAND2 protein appears to have a truncated central helix.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016470381  48 PETFRQQFRQFGYQDSPGPHEALSRLWELCHLWLRPEVHTKEQILELLVLEQFLAILPKELQAWVQKHHPENGEETVTML 127
Cdd:cd07936     1 PETYRQRFRAFQYQEASGPREALQRLRELCRQWLRPEIHTKEQILELLVLEQFLIILPPEVQAWVRERKPESGEEAATLA 80

                  ..
gi 1016470381 128 ED 129
Cdd:cd07936    81 ED 82

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*
gi 1016470381 294 LIQHRRTHTGEKPYKCHDCGKAFSQ 318
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSFKS 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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1016470381 277 KPYaCDECAKAFSRSAILIQHRRTHTgekpYKCHDCGKAFSQSSNLFRH---RKRHIRKKVP 335
Cdd:cd20908     1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHclqVHKETLTKVP 57

leucine rich region;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016470381   48 PETFRQQFRQFGYQDSPGPHEALSRLWELCHLWLRPEVHTKEQILELLVLEQFLAILPKELQAWVQKHHPENGEETVTML 127
Cdd:smart00431   1 PEIFRQRFRQFRYQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLL 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1016470381  128 EDVERELDGPKQIFFG--RRKDMIAEKLAPSE 157
Cdd:smart00431  81 EDLERELDEPGQQVSAhvHGQEVLLEKMVPLG 112

SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several vertebrate proteins that contain C2H2 zinc finger motifs, many of which may be transcription factors playing roles in cell survival and differentiation. This protein-interaction domain is able to mediate homo- and hetero-oligomerization of SCAN-containing proteins. Some SCAN-containing proteins, including those of lower vertebrates, do not contain zinc finger motifs. It has been noted that the SCAN domain resembles a domain-swapped version of the C-terminal domain of the HIV capsid protein. This domain model features elements common to the three general groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B). The SCAND1 protein is truncated at the C-terminus with respect to this model, the SCAND2 protein appears to have a truncated central helix.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016470381  48 PETFRQQFRQFGYQDSPGPHEALSRLWELCHLWLRPEVHTKEQILELLVLEQFLAILPKELQAWVQKHHPENGEETVTML 127
Cdd:cd07936     1 PETYRQRFRAFQYQEASGPREALQRLRELCRQWLRPEIHTKEQILELLVLEQFLIILPPEVQAWVRERKPESGEEAATLA 80

                  ..
gi 1016470381 128 ED 129
Cdd:cd07936    81 ED 82

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*
gi 1016470381 294 LIQHRRTHTGEKPYKCHDCGKAFSQ 318
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSFKS 26

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*.
gi 1016470381 265 ALILHQRIHSGKKPYACDECAKAFSR 290
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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1016470381 277 KPYaCDECAKAFSRSAILIQHRRTHTgekpYKCHDCGKAFSQSSNLFRH---RKRHIRKKVP 335
Cdd:cd20908     1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHclqVHKETLTKVP 57

hypothetical protein

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1016470381 278 PYACDECAKAFSRSAILIQHRRTHTGEKpyKCHDCGKAFSQSSNLFRHR-KRH 329
Cdd:PHA00733   73 PYVCPLCLMPFSSSVSLKQHIRYTEHSK--VCPVCGKEFRNTDSTLDHVcKKH 123