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PlantRegMap/PlantTFDB v5.0
Plant Transcription
Factor Database
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Home TFext BLAST Prediction Download Help About Links PlantRegMap |
Transcription Factor Information
Basic Information? help Back to Top | |||||||||
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TF ID | GSBRNA2T00125332001 | ||||||||
Common Name | GSBRNA2T00125332001 | ||||||||
Organism | |||||||||
Taxonomic ID | |||||||||
Taxonomic Lineage |
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
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Family | C2H2 | ||||||||
Protein Properties | Length: 1324aa MW: 147717 Da PI: 6.983 | ||||||||
Description | C2H2 family protein | ||||||||
Gene Model |
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Signature Domain? help Back to Top | |||||||
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No. | Domain | Score | E-value | Start | End | HMM Start | HMM End |
1 | zf-C2H2 | 11.2 | 0.0011 | 1206 | 1231 | 1 | 23 |
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sFs+ +L H r+ + GSBRNA2T00125332001 1206 YQCDmeGCTMSFSSEKQLSLHKRNiC 1231 99********************9877 PP | |||||||
2 | zf-C2H2 | 15.1 | 6.5e-05 | 1231 | 1253 | 3 | 23 |
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H+r+H GSBRNA2T00125332001 1231 CPvkGCGKNFFSHKYLVQHQRVH 1253 9999*****************99 PP |
Protein Features ? help Back to Top | ||||||
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Database | Entry ID | E-value | Start | End | InterPro ID | Description |
SMART | SM00545 | 4.1E-17 | 19 | 60 | IPR003349 | JmjN domain |
PROSITE profile | PS51183 | 14.284 | 20 | 61 | IPR003349 | JmjN domain |
Pfam | PF02375 | 1.6E-15 | 21 | 54 | IPR003349 | JmjN domain |
SMART | SM00558 | 1.7E-54 | 198 | 367 | IPR003347 | JmjC domain |
PROSITE profile | PS51184 | 34.513 | 201 | 367 | IPR003347 | JmjC domain |
SuperFamily | SSF51197 | 1.15E-27 | 213 | 384 | No hit | No description |
Pfam | PF02373 | 2.3E-37 | 231 | 350 | IPR003347 | JmjC domain |
Gene3D | G3DSA:3.30.160.60 | 9.7E-4 | 1205 | 1228 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
SMART | SM00355 | 9.4 | 1206 | 1228 | IPR015880 | Zinc finger, C2H2-like |
PROSITE profile | PS50157 | 13.609 | 1229 | 1258 | IPR007087 | Zinc finger, C2H2 |
SMART | SM00355 | 0.01 | 1229 | 1253 | IPR015880 | Zinc finger, C2H2-like |
Gene3D | G3DSA:3.30.160.60 | 2.0E-7 | 1230 | 1257 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
PROSITE pattern | PS00028 | 0 | 1231 | 1253 | IPR007087 | Zinc finger, C2H2 |
SuperFamily | SSF57667 | 6.4E-11 | 1245 | 1287 | No hit | No description |
Gene3D | G3DSA:3.30.160.60 | 2.3E-10 | 1258 | 1282 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
PROSITE profile | PS50157 | 11.801 | 1259 | 1288 | IPR007087 | Zinc finger, C2H2 |
SMART | SM00355 | 0.0015 | 1259 | 1283 | IPR015880 | Zinc finger, C2H2-like |
PROSITE pattern | PS00028 | 0 | 1261 | 1283 | IPR007087 | Zinc finger, C2H2 |
SuperFamily | SSF57667 | 2.19E-8 | 1277 | 1311 | No hit | No description |
Gene3D | G3DSA:3.30.160.60 | 6.7E-10 | 1283 | 1312 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
PROSITE profile | PS50157 | 10.492 | 1289 | 1320 | IPR007087 | Zinc finger, C2H2 |
SMART | SM00355 | 1.7 | 1289 | 1315 | IPR015880 | Zinc finger, C2H2-like |
PROSITE pattern | PS00028 | 0 | 1291 | 1315 | IPR007087 | Zinc finger, C2H2 |
Gene Ontology ? help Back to Top | ||||||
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GO Term | GO Category | GO Description | ||||
GO:0003676 | Molecular Function | nucleic acid binding | ||||
GO:0046872 | Molecular Function | metal ion binding |
Sequence ? help Back to Top |
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Protein Sequence Length: 1324 aa Download sequence Send to blast |
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPMAYICKI EEEASRYGIC KIVPPVPPSS 60 KKTAINNLNR SLAARARARA RDGGKPDYDG GPTFTTRQQQ IGFCPRRQRP VQRPVWQSGE 120 RYTFDEFEFK AKNFEKSYLK KCGKKGSVSP LEVETLYWRA SVDKPFSVEY ANDMPGSAFV 180 PLSLAAARRR ESGGDCGTVG ETAWNMRAMA RAEGSLLKFM KEEIPGVTSP MVYIAMMFSW 240 FAWHVEDHDL HSLNYLHMGA GKTWYGVPKD AAMAFEEVVR VHGYGEELNP LVTFSTLGEK 300 TTVMSPEVFV RAGIPCCRLV QNPGDFVITF PGAYHSGFSH GFNFGEASNI ATPQWLRMAK 360 DAAIRRASIN YPPMVSHLQL LYDYALALGS RVPDSIHNKP RSSRLKDKKK SEGEKLTNEL 420 FVQNIIHNNE LLHSLGKGSP IALLPQSSSD VSVCSDVRIG SHLGANQGQT TLLIKSEDLS 480 SDSVMVSLSN GDETQGTSTD VERRKNNGAV GLSDQRLFSC VTCGVLSFDC VAIIQPKEAA 540 ARYLMSADCS FLNDWTVASG SGNLGQDVVM PPSENTGKQD VGDLYNAPVQ TPYHSTTKTV 600 DQRTSSSSLT KESGALGLLA SAYGDSSDSE EEDHKGLDNP VSDEVACVLE ASSFVTDGND 660 EAGNGLSSAL NSQGLTCEKG KEVDVSHANL SKGGNASSVE ITLPFIPRSD DDFSRLHVFC 720 LEHAAEVEQR LHPIGGINIM LLCHPDYPRI EAEGKVVAKE LGVNHEWSYT EFKNVTREDE 780 ETIQAALANV EAKAGNSDWA VKLGINLSHS AILSRSPLYS KQMPYNSVIY NVFGRTSPAT 840 PQVSGIRSSR QRKYVAGKWC GKVWMSHQVH PFLLEEDLEG EETERSHLRA ALDEDVTVHG 900 NDSRDATTMF GRKYSRKRKA RGKVAPRKKL TSFKREAGVS DDTSEDHSYK QQWRAYGDEE 960 ESYLETGNEV SGDSSNQMSD QQQLKGVESD DDEVSERSLG QEYAVRREYA SSESSMENGF 1020 QVYREKQPMY DDDDDMYRHP RGIPRSKRTK VFRDLVSYDS EDQQRERVFT SDAQTSRMDD 1080 EYDSEENSLE EQDFCSSGKR QTRSIAKRKV KTKIVQSLGD TGGRTLLQSG SRKKMKELDS 1140 YMEGPSTRLR VRTPKPSRGS SATKPKKTGK KGRNVSFSEV VSEEEVEENE EESEEASTRI 1200 RECLPYQCDM EGCTMSFSSE KQLSLHKRNI CPVKGCGKNF FSHKYLVQHQ RVHSDERPLK 1260 CPWKGCKMTF KWAWSRTEHI RVHTGERPYV CAEPGCSQTF RFVSDFSRHK RKTGHSAKKI 1320 KKK* |
3D Structure ? help Back to Top | ||||||
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PDB ID | Evalue | Query Start | Query End | Hit Start | Hit End | Description |
6a57_A | 9e-74 | 1203 | 1323 | 20 | 140 | Lysine-specific demethylase REF6 |
6a58_A | 9e-74 | 1203 | 1323 | 20 | 140 | Lysine-specific demethylase REF6 |
6a59_A | 9e-74 | 1203 | 1323 | 20 | 140 | Lysine-specific demethylase REF6 |
6ip0_A | 2e-70 | 9 | 390 | 4 | 355 | Transcription factor jumonji (Jmj) family protein |
6ip4_A | 2e-70 | 9 | 390 | 4 | 355 | Arabidopsis JMJ13 |
Search in ModeBase |
Nucleic Localization Signal ? help Back to Top | |||
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No. | Start | End | Sequence |
1 | 916 | 928 | KRKARGKVAPRKK |
Expression -- Description ? help Back to Top | ||||||
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Source | Description | |||||
Uniprot | TISSUE SPECIFICITY: Highly expressed in the shoot apical meristem and primary and secondary root tips, and lower expression in cotyledons, leaves and root axis along vascular tissues. Detected in inflorescences, stems and siliques. {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18713399}. |
Functional Description ? help Back to Top | ||||||
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Source | Description | |||||
UniProt | Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3. Demethylates both tri- (H3K27me3) and di-methylated (H3K27me2) H3K27me (PubMed:21642989, PubMed:27111035). Demethylates also H3K4me3/2 and H3K36me3/2 in an in vitro assay (PubMed:20711170). Involved in the transcriptional regulation of hundreds of genes regulating developmental patterning and responses to various stimuli (PubMed:18467490). Binds DNA via its four zinc fingers in a sequence-specific manner, 5'-CTCTGYTY-3', to promote the demethylation of H3K27me3 and the regulation of organ boundary formation (PubMed:27111034, PubMed:27111035). Involved in the regulation of flowering time by repressing FLOWERING LOCUS C (FLC) expression (PubMed:15377760). Interacts with the NF-Y complexe to regulate SOC1 (PubMed:25105952). Mediates the recruitment of BRM to its target loci (PubMed:27111034). {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18467490, ECO:0000269|PubMed:20711170, ECO:0000269|PubMed:21642989, ECO:0000269|PubMed:25105952, ECO:0000269|PubMed:27111034, ECO:0000269|PubMed:27111035}. |
Cis-element ? help Back to Top | |
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Source | Link |
PlantRegMap | GSBRNA2T00125332001 |
Regulation -- PlantRegMap ? help Back to Top | ||||||
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Source | Upstream Regulator | Target Gene | ||||
PlantRegMap | Retrieve | - |
Annotation -- Protein ? help Back to Top | |||||||
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Source | Hit ID | E-value | Description | ||||
Refseq | XP_009149819.1 | 0.0 | PREDICTED: lysine-specific demethylase REF6 isoform X1 | ||||
Swissprot | Q9STM3 | 0.0 | REF6_ARATH; Lysine-specific demethylase REF6 | ||||
TrEMBL | A0A078F414 | 0.0 | A0A078F414_BRANA; BnaA06g16550D protein | ||||
STRING | Bra018060.1-P | 0.0 | (Brassica rapa) |
Orthologous Group ? help Back to Top | |||
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Lineage | Orthologous Group ID | Taxa Number | Gene Number |
Malvids | OGEM5259 | 28 | 43 |
Best hit in Arabidopsis thaliana ? help Back to Top | ||||||
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Hit ID | E-value | Description | ||||
AT3G48430.1 | 0.0 | relative of early flowering 6 |