PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Cotton_A_18629_BGI-A2_v1.0
Common NameF383_11209
Organism
Gossypium arboreum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium
Family C2H2
Protein Properties Length: 1563aa    MW: 177287 Da    PI: 8.8385
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cotton_A_18629_BGI-A2_v1.0genomeBGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.80.0003514731495323
                                  ET..TTTEEESSHHHHHHHHHHT CS
                     zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                                  Cp   Cgk F ++ +L++H r+H
  Cotton_A_18629_BGI-A2_v1.0 1473 CPvkGCGKKFFSHKYLVQHRRVH 1495
                                  9999*****************99 PP
2zf-C2H2120.0006215311557123
                                  EEET..TTTEEESSHHHHHHHHHH..T CS
                     zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                                  y+C+   Cg++F+  s++ rH r+  H
  Cotton_A_18629_BGI-A2_v1.0 1531 YVCSeeGCGQTFRFVSDFSRHKRKtgH 1557
                                  99********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005455.3E-152465IPR003349JmjN domain
PROSITE profilePS5118313.5362566IPR003349JmjN domain
PfamPF023753.5E-142659IPR003349JmjN domain
PROSITE profilePS5118430.707200343IPR003347JmjC domain
SMARTSM005587.1E-40200343IPR003347JmjC domain
SuperFamilySSF511972.09E-23214360No hitNo description
PfamPF023734.4E-10233269IPR003347JmjC domain
PfamPF023731.5E-15272326IPR003347JmjC domain
SMARTSM003558.414481470IPR015880Zinc finger, C2H2-like
SMARTSM003550.004514711495IPR015880Zinc finger, C2H2-like
SuperFamilySSF576674.55E-614711508No hitNo description
PROSITE profilePS5015712.36214711500IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.6E-514721499IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028014731495IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.603.7E-815001525IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.74115011530IPR007087Zinc finger, C2H2
SMARTSM003550.001415011525IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028015031525IPR007087Zinc finger, C2H2
SuperFamilySSF576672.35E-915111555No hitNo description
Gene3DG3DSA:3.30.160.602.1E-915261554IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.1715311557IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.21715311562IPR007087Zinc finger, C2H2
PROSITE patternPS00028015331557IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0032259Biological Processmethylation
GO:0003676Molecular Functionnucleic acid binding
GO:0008168Molecular Functionmethyltransferase activity
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 1563 aa     Download sequence    Send to blast
MACSSHHSLE QSQEAFSWLK SMPLAPEYRP TLAEFQDPIA YIFKIEKEAS QYGICKIIPP  60
VPPASKKTAI GNLNRSLLAR AEANASSDLK PTPTFTTRQQ QIGFCPRKPR PVQKPVWQSG  120
EYYTFQEFEA KAKSFERNYL KKYSKKGTLS ALEVETLFWK ATVDKPAMVE YANDMPGSAF  180
VPLNPKKSSG GGREAGEGAT VGETPWNMRA VSRAKGSLLR FMKEEIPGVT SPMVYIAMLF  240
SWFAWHVEDH DLHSLNYLHM GAGKTWYVTF STLGEKTTVM SPEVFLHAGI PCCRLVQNAG  300
EFVVTFPRAY HSGFSHGFNF GEAANIATPE WLRVARDAAI RRASINYPPM VSHFQLLYDL  360
ALELCSRIPM SISAKPKSSR LKDKRKNEGE NLVKELFVQN LIQNNNLLHI LGKGSSVVLL  420
PKSSPDISLC SDLRCQSRIN PRMSLSLYKD IIKSSKDVGS DETVIGGNEE IKGIKGFYSV  480
KGNFASMYEG NRDSSFSGND YSCRFPSQTS NTIRERDSAI LGDALPDQRL FSCVTCGILC  540
FACVAVLQPT DQAARYLMSA DCSFFNDWTV GSGVTHDGFN AAHGDAITSE QNPCSRRMNK  600
SAPNSLYDVS VQPVDSKFRM GDQSTQVLED TEKRGESSAL GLLASTYGNS SDSEEDRPEP  660
NATIFHDETN PTNVSPERKI QYNDSGFSPS EVNTSRNPSL SRLNSEEESP FDIKNGSPET  720
FDPDLEFKTD NLISRRSNGL EDKFRDPMTS SHVNPNYSRA AHGIEKMRFS MAVLPMENVD  780
IPCIQRTDED SSRMHVFCLE HAVEVEQQLR QIGGVQVFLL CHPEYPRIEA EAKLVAEELG  840
IDYPWNDILF GDATKDDKER IQSALDSEDS IPGNGDWAVK LGINLFYSAN LSRSTLYSKQ  900
MPYNWIIYSA FGRNSSDSSP KKLNVYGRRS GKPRKVVAGK WCGKVWMSNQ VHPFLAQRDP  960
EEQEQERSFH AQAISDENVE RKPENVLKAE TMKVVNRKRK SRAEITLNKK VKRVESEGAV  1020
SDDSLDGSSL RQQQIVFRGK KPRLVEKEET VSCDLLEDDS LLRHWNLSRN RRAKFIEREN  1080
AESEDAEEDF THQQQRSNLR GRHNKYIEED DEVSGDLLNE SSLKQYRRTP RSLQAKFSDG  1140
ENGVSDDEQE EISHKLHRRI PRGKQIKSSK RNTAVSDDSL KQYRRMRKGK QTKFFERDDA  1200
MSDYASDDDS QYQIRRIPRG KQMKCMERDD AFSDDSVEDN SQQQHQRILS NKAAKFTERR  1260
RVHRSQLTEF IEMEDAVSSD SPDDNSSLRQ PRRIPRSKQP EILEREDAIS DDSLDGSHQS  1320
NRSLRNRKKK GPTLCQMKQE TAQNVKQVKR RSTEQVISQQ VKQETPQNRN TKIKQTARHC  1380
SSSSDEDEIE EGGPSTRLRK RTRKPPKQLE TKPKEKKQAG KKKVKHALNS KTLSGQNSAK  1440
VRDEEVEYQC DMEGCSMSFG SKQALLLHKR NICPVKGCGK KFFSHKYLVQ HRRVHLDDRP  1500
LKCPWKGCKM TFKWAWARTE HIRVHTGARP YVCSEEGCGQ TFRFVSDFSR HKRKTGHSGK  1560
KGS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A3e-671448156123136Lysine-specific demethylase REF6
6a58_A3e-671448156123136Lysine-specific demethylase REF6
6a59_A3e-671448156123136Lysine-specific demethylase REF6
6ip0_A4e-66183648353Transcription factor jumonji (Jmj) family protein
6ip4_A4e-66183648353Arabidopsis JMJ13
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtHistone 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}.
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJX5776345e-98JX577634.1 Gossypium hirsutum clone NBRI_GE9494 microsatellite sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_017605239.10.0PREDICTED: lysine-specific demethylase JMJ705-like
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A0B0MHK50.0A0A0B0MHK5_GOSAR; Lysine-specific demethylase REF6-like protein
STRINGGorai.001G061900.10.0(Gossypium raimondii)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM52592843
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G48430.10.0relative of early flowering 6
Publications ? help Back to Top
  1. Li C, et al.
    Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 687-93
    [PMID:27111034]
  2. Cui X, et al.
    REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 694-9
    [PMID:27111035]
  3. Hyun Y, et al.
    Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem.
    Dev. Cell, 2016. 37(3): p. 254-66
    [PMID:27134142]
  4. Cheng JZ,Zhou YP,Lv TX,Xie CP,Tian CE
    Research progress on the autonomous flowering time pathway in Arabidopsis.
    Physiol Mol Biol Plants, 2017. 23(3): p. 477-485
    [PMID:28878488]
  5. Li C, et al.
    Verification of DNA motifs in Arabidopsis using CRISPR/Cas9-mediated mutagenesis.
    Plant Biotechnol. J., 2018. 16(8): p. 1446-1451
    [PMID:29331085]
  6. Wang X, et al.
    The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis.
    PLoS Genet., 2019. 15(4): p. e1008068
    [PMID:30969965]
  7. Qiu Q, et al.
    DNA methylation repels targeting of Arabidopsis REF6.
    Nat Commun, 2019. 10(1): p. 2063
    [PMID:31048693]