SSXRD motif; SSX1 can repress transcription, and this has been attributed to a putative Kruppel associated box (KRAB) repression domain at the N-terminus. However, from the analysis of these deletion constructs further repression activity was found at the C-terminus of SSX1. Which has been called the SSXRD (SSX Repression Domain). The potent repression exerted by full-length SSX1 appears to localize to this region.

                          10        20
                  ....*....|....*....|....*..
gi 1907123478 145 NVEVKMYRLRERKGLAYEEVSEPQDDD 171
Cdd:pfam09514   5 EVEVWMYRLRERKGVVYEEISDPQEDD 31

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 1907123478  32 FKDISIYFSKEEWAEMGEWEKIRYRNVKR-NYKMLISI 68
Cdd:cd07765     3 FEDVAVYFSQEEWELLDPAQRDLYRDVMLeNYENLVSL 40

SSXRD motif; SSX1 can repress transcription, and this has been attributed to a putative Kruppel associated box (KRAB) repression domain at the N-terminus. However, from the analysis of these deletion constructs further repression activity was found at the C-terminus of SSX1. Which has been called the SSXRD (SSX Repression Domain). The potent repression exerted by full-length SSX1 appears to localize to this region.

                          10        20
                  ....*....|....*....|....*..
gi 1907123478 145 NVEVKMYRLRERKGLAYEEVSEPQDDD 171
Cdd:pfam09514   5 EVEVWMYRLRERKGVVYEEISDPQEDD 31

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 1907123478  32 FKDISIYFSKEEWAEMGEWEKIRYRNVKR-NYKMLISI 68
Cdd:cd07765     3 FEDVAVYFSQEEWELLDPAQRDLYRDVMLeNYENLVSL 40

krueppel associated box;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907123478   32 FKDISIYFSKEEWAEMGEWEKIRYRNV-KRNYKMLISI---VSPPWVPFRVKHSKQQ 84
Cdd:smart00349   3 FEDVAVYFTQEEWEQLDPAQKNLYRDVmLENYSNLVSLgfqVPKPDLISQLEQGEEP 59

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*.
gi 1907123478 521 HLIQHQRTHTGEKPYVCRECGRGFTQ 546
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 1907123478 729 KPYvCRECGRGFTAKSVLIQHQRTHTgekpYVCRECGRGFTQKSNLIKH 777
Cdd:cd20908     1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVH 44

PR-SET domain found in PRDM (PRDI-BF1 and RIZ homology domain) family of proteins; PRDM family of proteins is defined based on the conserved N-terminal PR domain, which is closely related to the Su(var)3-9, enhancer of zeste, and trithorax (SET) domains of histone methyltransferases, and is specifically called PR-SET domain. The family consists of 17 members in primates. PRDMs play diverse roles in cell-cycle regulation, differentiation, and meiotic recombination. The family also contains zinc finger protein ZFPM1 and ZFPM2. ZFPM1 (also termed friend of GATA protein 1, FOG-1, friend of GATA 1, zinc finger protein 89A, or zinc finger protein multitype 1) functions as a transcription regulator that plays an essential role in erythroid and megakaryocytic cell differentiation. ZFPM2 (also termed friend of GATA protein 2, FOG-2, friend of GATA 2, zinc finger protein 89B, or zinc finger protein multitype 2) functions as a transcription regulator that plays a central role in heart morphogenesis and development of coronary vessels from epicardium, by regulating genes that are essential during cardiogenesis.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907123478 212 LPPGLRISPSGIPEAGLGVWNEAsDLPVGLHFGPYEGQItedeeaansgyswlitkgrncyeyvdgqdesqaNWMRYVNC 291
Cdd:cd10534     1 LPAGLELVLSSIPEGGLGVFARR-TIPAGTRFGPLEGVV---------------------------------NWMRFVRP 46

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1907123478 292 ARDDEEQNLVAFQYHRKIFYRTCRVIRPGCELLVWYG 328
Cdd:cd10534    47 ARNEEEQNLVAYQHGGQIYFRTTRDIPPGEELLVWYS 83

PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins; PRDM11 (also termed PR domain-containing protein 11) may be involved in transcription regulation.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907123478 210 LSLPPGLRISPSGIPEAGLGVWNEAsdLPVGLHFGPYEGQITEDEEAANSgYSWLITKGRNCYEYVDGQDESQANWMRYV 289
Cdd:cd19195     3 LTAPQGIEVVKDTSGESDVRCVDEV--IPKGHIFGPYEGQICTQDKSSGF-FSWLIVDKNNRYKSIDGSDETKANWMRYV 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1907123478 290 NCARDDEEQNLVAFQYHRKIFYRTCRVIRPGCELLVWYGDEYGQEL 335
Cdd:cd19195    80 VISREEREQNLLAFQHSEQIYFRACRDIRPGEKLRVWYSEDYMKRL 125

PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins; PRDM2 (also termed GATA-3-binding protein G3B, lysine N-methyltransferase 8, MTB-or MTE-binding protein, PR domain-containing protein 2, retinoblastoma protein-interacting zinc finger protein, or zinc finger protein RIZ) is S-adenosyl-L-methionine-dependent histone methyltransferase that specifically methylates 'Lys-9' of histone H3. It may function as a DNA-binding transcription factor.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907123478 212 LPPGLRISPSGIPEAGLGVWNEASdLPVGLHFGPYEGQITEDEEAANSGYSWLITKGRNCYEYVDGQDESQANWMRYVNC 291
Cdd:cd19188     4 LPEELELKPSAVDKTRIGVWAKKS-IPKGRKFGPFVGEKKKRSQVKNNVYMWEIYGPKRGWMCVDASDPTKGNWLRYVNW 82

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1907123478 292 ARDDEEQNLVAFQYHRKIFYRTCRVIRPGCELLVWYGDE 330
Cdd:cd19188    83 ARSGEEQNLFPLQINRAIYYKTLKPIAPGEELLCWYNGE 121

PR-SET domain found in PR domain zinc finger protein 6 (PRDM6) and similar proteins; PRDM6 (also termed PR domain-containing protein 6) is a putative histone-lysine N-methyltransferase that acts as a transcriptional repressor of smooth muscle gene expression. It may specifically methylate 'Lys-20' of histone H4 when associated with other proteins and in vitro.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907123478 212 LPPGLRISPSGIPEAGLGVWnEASDLPVGLHFGPYEGQITEDEE----AANSGYSWLI--TKGRNCYeYVDGQDESQANW 285
Cdd:cd19191     1 LPDEVCLCTSSIPGLGYGIC-AAQRIPQGTWIGPFEGVLVSPEKqigaVRNTQHLWEIydQEGTLQH-FIDGGDPSKSSW 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1907123478 286 MRYVNCARDDEEQNLVAFQYHRKIFYRTCRVIRPGCELLVWYGDEYGQ 333
Cdd:cd19191    79 MRYIRCARHCGEQNLTVVQYRGCIFYRACRDIPRGTELLVWYDDSYTS 126

PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins; PRDM4 (also termed PR domain-containing protein 4, or PFM1) may function as a transcription factor involved in cell differentiation.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907123478 210 LSLPPGLRISPSgIPEAGLGVWNEASdLPVGLHFGPYEGQIT-----EDEEAANSGYSWLITKGRNCYEYVDGQDESQAN 284
Cdd:cd19189     4 LSLPRQLYLRQS-ETGAEVGVWTKET-IPVRTCFGPLIGQQShsaevADWTDKAAPHIWKIYHNDVLEFCIITTDENECN 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1907123478 285 WMRYVNCARDDEEQNLVAFQYHRKIFYRTCRVIRPGCELLVWYGDEYGQELG 336
Cdd:cd19189    82 WMMFVRKARTREEQNLVAYPHDGKIYFCTSRDIPPDQELLFYYSRDYARQLG 133

PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins; PRDM15 (also termed PR domain-containing protein 15, or zinc finger protein 298 (ZNF298)) may be involved in transcriptional regulation. It plays an essential role as a chromatin factor that modulates the transcription of upstream regulators of WNT and MAPK-ERK signaling to safeguard naive pluripotency.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907123478 210 LSLPPGLRISPsgIPEAGLGVWnEASDLPVGLHFGPYEGQITE--DEEAANSGYswLITKGRNCYeYVDGQDESQANWMR 287
Cdd:cd19199     5 SSLPDNLEIRQ--LEDGSEGVF-ALVPLVKRTQFGPFEAKRVArlDGFAVFPLK--VFEKDGSVV-YLDTSNEDDCNWMM 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1907123478 288 YVNCARDDEEQNLVAFQYHRKIFYRTCRVIRPGCELLVWYGDEY 331
Cdd:cd19199    79 FVRPATDVEHQNLTAYQQGEDIYFTTSRDIQPGAELRVWYAAFY 122

PR-SET domain found in PR domain zinc finger protein 8 (PRDM8) and similar proteins; PRDM8 (also termed PR domain-containing protein 8) may function as histone methyltransferase, preferentially acting on 'Lys-9' of histone H3.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907123478 218 ISPSGIPEAGL---------GVWNeASDLPVGLHFGPYEGQITEDEEAANSGyswLITKGRNCYEYVDGQDESQAN---- 284
Cdd:cd19192     1 MSHRSLWRGGSksvltdiftSVVT-TTDIPAGTIFGPCVLSFTLGYDIADIA---LKTTDKRVVPYIFRVDTGACNgsse 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1907123478 285 ---WMRYVNCARDDEEQNLVAFQY-HRKIFYRTCRVIRPGCELLVWYGDE 330
Cdd:cd19192    77 psdWLRLVQPARDRHEQNLEAFRKnEGQVYFRTLRRIRKGEELLVWYSDE 126

PR-SET domain found in PR domain zinc finger protein 16 (PRDM16) and similar proteins; PRDM16, also termed PR domain-containing protein 16, or transcription factor MEL1, or MDS1/EVI1-like gene 1, functions as a transcriptional regulator. PRDM16 is preferentially expressed by hematopoietic and neuronal stem cells and is closely related to paralog of PRDM3, both of which are directly linked to various aspects of oncogenic transformation.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907123478 212 LPPGLRISPSGIPEAGLGVWNEaSDLPVGLHFGPYEG--------------QITED-EEAANSGYSWLITKGRNCYEY-V 275
Cdd:cd19213    20 IPSDFELRESSIPGAGLGVWAK-RKIEAGERFGPYTGvqrstlkdtnfgweQILNDvEVSSQEGCITKIVDDLGNEKFcV 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907123478 276 DGQDESQANWMRYVNCARDDEEQNLVAFQYHRKIFYRTCRVIRPGCELLVWYGD 329
Cdd:cd19213    99 DAGQAGAGSWLKYIRVACSCDEQNLTACQINEQIYYKVIKDIEPGEELLVYVKD 152

PR-SET domain found in PR domain zinc finger protein 13 (PRDM13) and similar proteins; PRDM13 (also termed PR domain-containing protein 13) may be involved in transcriptional regulation. It mediates the balance of inhibitory and excitatory neurons in somatosensory circuits.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907123478 275 VDGQDESQANWMRYVNCARDDEEQNLVAFQYHR--KIFYRTCRVIRPGCELLVWYG 328
Cdd:cd19197    41 VDESGSPATEWIGLVRAARNNQEQNLEAIADLPggQIFYRALRDIQPGEELTVWYS 96

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907123478 505 KPYVCRECGRGFTQNSHLIQHQRTHTGEKPYVCRECGRGFTQK--SDLIKHQRTHTGEKPYvcRECGRGFTQKSDLIKHQ 582
Cdd:COG5048    32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSrpLELSRHLRTHHNNPSD--LNSKSLPLSNSKASSSS 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907123478 583 RTHTGEKPYV---CRECGRGFTQKSVLIKHQRTHTGEKPYVCRECGRGF--TQKSVLIKHQRTHTgekpyvcRECGRGFT 657
Cdd:COG5048   110 LSSSSSNSNDnnlLSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSSvnTPQSNSLHPPLPAN-------SLSKDPSS 182

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907123478 658 AKSVLIQHQRTHTGEKPYVCRECGRgFTAKSNLIQHQRTHTGEKPYVCRECGRGFTAKSVLIQHQRTHTGEKPYVCRECG 737
Cdd:COG5048   183 NLSLLISSNVSTSIPSSSENSPLSS-SYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDSSSSASESP 261

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907123478 738 RGFTAKSVLIQHQRTHTGE-------KPYVCRECGRGFTQKSNLIKHQRT--HTGE--KPYVCRE--CGWGFTQKSDLIQ 804
Cdd:COG5048   262 RSSLPTASSQSSSPNESDSssekgfsLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPYslCGKLFSRNDALKR 341

                  ....*.
gi 1907123478 805 HQRTHT 810
Cdd:COG5048   342 HILLHT 347

SET domain found in Legionella pneumophila type IV secretion system effector LegAS4 and similar proteins; LegAS4 is a type IV secretion system effector of Legionella pneumophila. It contains a SET domain that is involved in the modification of Lys4 of histone H3 (H3K4) in the nucleolus of the host cell, thereby enhancing heterochromatic rDNA transcription. It also contains an ankyrin repeat domain of unknown function at its C-terminal region.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907123478 217 RISPSGIP---EAGLGVWnEASDLPVGLHFGPYEG-QITEDEEAANS----GYSWLITKGRNCYeYVDGqdESQANWMRY 288
Cdd:cd10522     1 KVDISMIPnlsHNGLGLF-AAETIAKGEFVGEYTGeVLDRWEEDRDSvyhyDPLYPFDLNGDIL-VIDA--GKKGNLTRF 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1907123478 289 VNCARDDeeqNLVAFQYHRK----IFYRTCRVIRPGCELLVWYGDEY 331
Cdd:cd10522    77 INHSDQP---NLELIVRTLKgeqhIGFVAIRDIKPGEELFISYGPKY 120

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on outlier plant homologues

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907123478  216 LRISPSgiPEAGLGVWNeASDLPVGLHFGPYEGQITEDEEAANSG--YSWLITKGRNCYE-----YVDGQdeSQANWMRY 288
Cdd:smart00317   3 LEVFKS--PGKGWGVRA-TEDIPKGEFIGEYVGEIITSEEAEERPkaYDTDGAKAFYLFDidsdlCIDAR--RKGNLARF 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1907123478  289 VNCARDDEEQNLVAFQ-YHRKIFYRTCRVIRPGCELLVWYGDEYGQE 334
Cdd:smart00317  78 INHSCEPNCELLFVEVnGDDRIVIFALRDIKPGEELTIDYGSDYANE 124

PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins; PRDM5 (also termed PR domain-containing protein 5) is a sequence-specific DNA-binding transcription factor that represses transcription at least in part by recruitment of the histone methyltransferase EHMT2/G9A and histone deacetylases such as HDAC1.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907123478 227 GLGVWNeASDLPVGLHFGPYEGQ---ITEDEEAANSGYSWLI--TKGRNCYeYVDGQDESQANWMRYVNCARDDEEQNLV 301
Cdd:cd19190    19 GMGLYT-ARRVKKGEKFGPFAGEkrmPNELDESMDPRLMWEVrgSKGEVLY-ILDASNPRHSNWLRFVHEAPSQEQKNLA 96

                          90       100
                  ....*....|....*....|....*...
gi 1907123478 302 AFQYHRKIFYRTCRVIRPGCELLVWYGD 329
Cdd:cd19190    97 AIQEGENIFYLAVDDIETDTELLIGYLD 124

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*.
gi 1907123478 521 HLIQHQRTHTGEKPYVCRECGRGFTQ 546
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 1907123478 759 YVCRECGRGFTQKSNLIKHQRTH 781
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*
gi 1907123478 746 LIQHQRTHTGEKPYVCRECGRGFTQ 770
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSFKS 26

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*.
gi 1907123478 549 DLIKHQRTHTGEKPYVCRECGRGFTQ 574
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 1907123478 535 YVCRECGRGFTQKSDLIKHQRTH 557
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*.
gi 1907123478 493 NVNEHQKTHTGEKPYVCRECGRGFTQ 518
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....
gi 1907123478 662 LIQHQRTHTGEKPYVCRECGRGFT 685
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSFK 25

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 1907123478 729 KPYvCRECGRGFTAKSVLIQHQRTHTgekpYVCRECGRGFTQKSNLIKH 777
Cdd:cd20908     1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVH 44

PR-SET domain found in zinc finger protein ZFPM1 and similar proteins; ZFPM1 (also termed friend of GATA protein 1, FOG-1, friend of GATA 1, zinc finger protein 89A, or zinc finger protein multitype 1) functions as a transcription regulator that plays an essential role in erythroid and megakaryocytic cell differentiation.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907123478 236 DLPVGLHFGPYEGQIT----EDEEAANSGYSWLITKGRNCyeyvdgqdesqanWMRYVNCARDDEEQNLVAFQYHRKIFY 311
Cdd:cd19215    23 SLSEGLSWGPYHGSIQssasSPGQAEESPAVTLLLVDEDC-------------WLRRLPLVSTEAEANCTIYRKGDAIWC 89

                          90
                  ....*....|....
gi 1907123478 312 RTCRVIRPGCELLV 325
Cdd:cd19215    90 KTTKPVPEGELLSA 103

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 1907123478 787 YVCRECGWGFTQKSDLIQHQRTH 809
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 1907123478 675 YVCRECGRGFTAKSNLIQHQRTH 697
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 1907123478 619 YVCRECGRGFTQKSVLIKHQRTH 641
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 1907123478 701 KPYvCRECGRGFTAKSVLIQHQRTHTgekpYVCRECGRGFTAKSVLIQH 749
Cdd:cd20908     1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVH 44