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_09671_BGI-A2_v1.0
Common NameF383_05499
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: 1614aa    MW: 182626 Da    PI: 9.0696
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cotton_A_09671_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-C2H212.80.0003515151537323
                                  ET..TTTEEESSHHHHHHHHHHT CS
                     zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                                  Cp   Cgk F ++ +L++H r+H
  Cotton_A_09671_BGI-A2_v1.0 1515 CPvkGCGKKFFSHKYLVQHRRVH 1537
                                  9999*****************99 PP
2zf-C2H211.60.0008415731599123
                                  EEET..TTTEEESSHHHHHHHHHH..T CS
                     zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                                  y+C    Cg++F+  s++ rH r+  H
  Cotton_A_09671_BGI-A2_v1.0 1573 YVCAeeGCGQTFRFVSDFSRHKRKtgH 1599
                                  89********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005454.9E-132364IPR003349JmjN domain
PROSITE profilePS5118313.3142465IPR003349JmjN domain
PfamPF023751.7E-132558IPR003349JmjN domain
PROSITE profilePS5118433.783199368IPR003347JmjC domain
SMARTSM005586.9E-49199368IPR003347JmjC domain
SuperFamilySSF511971.46E-25213384No hitNo description
PfamPF023732.9E-35232351IPR003347JmjC domain
SMARTSM003552614901512IPR015880Zinc finger, C2H2-like
SMARTSM003550.004515131537IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.44515131542IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.4E-515141541IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028015151537IPR007087Zinc finger, C2H2
SuperFamilySSF576671.74E-915291571No hitNo description
Gene3DG3DSA:3.30.160.603.8E-815421567IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001415431567IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.74115431572IPR007087Zinc finger, C2H2
PROSITE patternPS00028015451567IPR007087Zinc finger, C2H2
SuperFamilySSF576675.45E-815611595No hitNo description
Gene3DG3DSA:3.30.160.603.3E-915681596IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.8515731599IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.78315731604IPR007087Zinc finger, C2H2
PROSITE patternPS00028015751599IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009741Biological Processresponse to brassinosteroid
GO:0009826Biological Processunidimensional cell growth
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0032259Biological Processmethylation
GO:0033169Biological Processhistone H3-K9 demethylation
GO:0035067Biological Processnegative regulation of histone acetylation
GO:0048366Biological Processleaf development
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0008168Molecular Functionmethyltransferase activity
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 1614 aa     Download sequence    Send to blast
MAASSLSPEP SQEVFPWLKY LPFAPEYRPT LVEFQDPIAY IFKIEKEASQ YGICKIIPPV  60
PPASKKAAIG NLNRSLLERA VVNASSDSKP APTFTTRQQQ IGFCPRKQRP VLKSVWQSGE  120
YYTFQEFEAK AKNFERNYLK KYSKKGSLSA LEIETLFWKA TVDQPFDIEY ANDMPGSAFA  180
ALSSKKSSGG GRETGEGVTV AETPWNMRAV SRAKGSLLRF MKEEIPGVTS PMVYIAMLFS  240
WFAWHVEDHD LHSLNYLHMG AGKTWYGVPR DAAVAFEEVV RVDGYAGEFN PLVTFSTLGE  300
KTTVMSPEVF VHAGIPCCRL VQNAGEFVVT FPRAYHSGFS HGFNLGEAAN IATPEWLRVA  360
RDAAIRRASI NYPPMVSHFQ LLYDLALDLC SRVPTNIGAK PKSSRLKDKK KCEGETLVKE  420
LFVQDLIQNN DLLHILGKGS SVVLLPKSST DISLCSESRV ASRLRINPKM SLGLCRYKEA  480
MKPSQVLAFD EIMQCKNEEI KGIKGFYSVK GKTVSTYEVD RDSSFTGADY LCKVPSQTLN  540
ANIERESSVQ GDTLSDQRLF TCVTCGILCF ACIAVLQPTE QAARYLMSAD CSFFNDWTFG  600
SGVTCDRFTA THGDGITSEQ NPSTRGMNKT APNALYDVPV QSVEDKFQMK NQSKEVPEDT  660
KERRNTSALG LLASTYGNSS DSEDDNVEPK ATASGDETNS TNTIPGRKLQ HNDFKEEAPV  720
HVFDCDPEPG SKRSPPTINQ ELVSNGLGDK CSDPTIESHG AEKMRFSKAF TQMENADSPF  780
APNSDEDSSR MHVFCLEHAI EVEQQLRQIG GVHIFLLCHP EYPKIEAEAK LVAEELGIDY  840
LWNNILFGDA TKDDEVRIRS ALDSEDAIPG NGDWAVKLGI NLFYSSNLSH SMLYSKQMPY  900
NSVIYSAFGR NSPTSSPTKL NSYGRRSRKQ KKVVAGKWCG KVWMSNQVHP FLTQRDPGEQ  960
EQEKSYHAWA TSDENLESKP ENIRKAETSK VAKRFTRKSK TRAGTTPSKK AKCIEPESVV  1020
SDDSLDGNSL RQQQRFFRGK KPKLIEKEKE ISYDSLDDDS LLHHRDLSRR KGAKFIEREA  1080
SESEDAEEDS DDQQFRKNLG GKQGKYIVEN DVVSGDSLDK TSAKQYRRIP RSCLAKFMKR  1140
EGSVSADEQE EISHQFHKRI PRGRHIKLFE RRLAVSDDSR ADNSLKQYRR MPKGKRAKFF  1200
EREEAMSDDA SDNDDSQTQH RRIPSGKQMK CMEREDEFSD DSLEDNPQQQ HRRIAQRKVS  1260
KFSDQEDIVS FDSLKGNSHR QHRRIPRSQL TQFIEREDAG SSDSPDDSSL QQLRRILRSK  1320
HAKILEKEDA VSDDSDDTSP QQFRKTPRSR QGKSIESEDV VSYDSSDENY GQPNSSFRSR  1380
KKKAPTPRQT KQKAPKNVKQ GKRRTTKQVI SQQSKQDTRR NRNTKIEQSA RQDNSYDEDE  1440
IEGGPSTRLR KRARKPSKEP ETKPKVKKQA LKNKAKSASN AKVRDEEAEY QCDMEGCTMS  1500
FGLKQELVLH KKNICPVKGC GKKFFSHKYL VQHRRVHMDD RPLKCPWKGC KMTFKWAWAR  1560
TEHIRVHTGA RPYVCAEEGC GQTFRFVSDF SRHKRKTGHS LKKGKEIKHE SRKL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A5e-73173898353Transcription factor jumonji (Jmj) family protein
6ip4_A5e-73173898353Arabidopsis 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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00608ChIP-seqTransfer from AT3G48430Download
Motif logo
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_017611137.10.0PREDICTED: lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A0B0P3560.0A0A0B0P356_GOSAR; Lysine-specific demethylase REF6-like protein
STRINGGorai.006G270100.10.0(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]