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 Csa06g022210.1
Organism
Camelina sativa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Camelina
Family C2H2
Protein Properties Length: 1366aa    MW: 153520 Da    PI: 7.2923
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Csa06g022210.1genomeCSGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.50.0009612481273123
                      EEET..TTTEEESSHHHHHHHHHH.T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                      y+C    C++sF++  +L  H r+ +
  Csa06g022210.1 1248 YQCDmeGCTMSFTSEKQLALHKRNiC 1273
                      99********************9877 PP
2zf-C2H216.91.8e-0512731295323
                      ET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                      Cp   CgksF ++ +L++H+r+H
  Csa06g022210.1 1273 CPvrGCGKSFFSHKYLVQHQRVH 1295
                      9999*****************99 PP
3zf-C2H213.60.0001913311357123
                      EEET..TTTEEESSHHHHHHHHHH..T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                      y+C   dCg++F+  s++ rH r+  H
  Csa06g022210.1 1331 YVCAepDCGQTFRFVSDFSRHKRKtgH 1357
                      899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005457.4E-171960IPR003349JmjN domain
PROSITE profilePS5118313.8132061IPR003349JmjN domain
PfamPF023755.7E-142154IPR003349JmjN domain
SMARTSM005581.5E-53200369IPR003347JmjC domain
PROSITE profilePS5118434.854203369IPR003347JmjC domain
SuperFamilySSF511972.31E-28215387No hitNo description
PfamPF023732.0E-38233352IPR003347JmjC domain
SMARTSM003558.512481270IPR015880Zinc finger, C2H2-like
SMARTSM003550.001812711295IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.42212711300IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.606.0E-712721299IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012731295IPR007087Zinc finger, C2H2
SuperFamilySSF576673.96E-1012871329No hitNo description
Gene3DG3DSA:3.30.160.609.7E-913001324IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001513011325IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.92813011330IPR007087Zinc finger, C2H2
PROSITE patternPS00028013031325IPR007087Zinc finger, C2H2
SuperFamilySSF576676.08E-813191353No hitNo description
Gene3DG3DSA:3.30.160.606.0E-913251354IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003551.113311357IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.40613311362IPR007087Zinc finger, C2H2
PROSITE patternPS00028013331357IPR007087Zinc 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: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:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 1366 aa     Download sequence    Send to blast
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASKYGIC KILPPLPPPS  60
KKTSISNLNR SLAARAVGRV RDGGFGVCDY DGGPTFATRQ QQIGFCPRKQ RPVQRPVWQS  120
GEEYSFGEFE FKAKTFEKNY LKKCGKKSQL SPLEIETLYW RATVDKPFSV EYANDMPGSA  180
FIPLSLAAAR RRESGGDGGT VGETAWNMRA MARAEGSLLK FMKEDIPGVT SPMVYIAMMF  240
SWFAWHVEDH DLHSLNYLHM GASKTWYGVP KEAAPAFEEV VRVHGYGGEL NPLVTFSTLG  300
EKTTVMSPEV FVKAGIPCCR LVQNPGEFVV TFPGAYHSGF SHGFNFGEAS NIATPQWLTM  360
AKDAAIRRAA INYPPMVSHL QLLYDFALAL GSRVPTSIIA KPRSSRLKDK KRSEGERLTK  420
KLFVENIIHN NELLSSLGKG SPVGLLPQSS SDISVCSDLR IGSDLRTNQE KPIQLKSEEF  480
SSDSVMVGLS NDLRDAVSVK EKFTSLCERN RNHLASGEKE THETLSDAER REKGGAARLS  540
DQRLFSCVTC GVLSFDCVAI IQPKEAAAKY IMSADSSFFN DWTAASGSAN LGQAARSHYP  600
QSLEKHDVNY FSNVPVQTGH ERSSTTSLTN ADKDNGALGL LVSAYGDSSD SEEEDNKGLD  660
ASTSEGERKE NACAFQASSF DTDGNEVARD GRTSDFNSQR LTSKQNSLTK GDNSSLLELT  720
LPFVPRSDDD PCQLHVFCLE HAAEVEQQLR DIGGIHIMLL CHPEYPRIEA EAKIVAEELA  780
VNHEWNDTEF RNVTREDEET IQTALDNVEA KGGNSDWTVK LGINLSYSAI LSRSPLYSKQ  840
MPYNSVIYNV FGRSSPAVSS LSKPEVSGKR SFRQRKYVVG KWCGKVWMSH QVHPFLLEED  900
LEGEEERSCH LRTAMDEDVT GKRLFPCNVS RDAATMFGRK YCRKRKVRAK AVPRKKLTSF  960
KREDEVSDDT SEDHSYKQQW RASGKEEESY FETGHTASGD SSNQMSDQRK EIARHKDYNG  1020
IESDEEVSDR SLGEEYTVRE RAVSESSMEN GFQPYREKQS MYDRDEDDED DDMYKHPREI  1080
PRSKRTKVFR NPVSYNSEVA GVYQQRGRVS RSSRQANRLG GEYDSPENSF EELDLCSTGK  1140
RQTRSTAKRK AKTKTVQSPR DTKSRTLQEF ASGMKTEDLD SYMEGPSTRL RVRNQKPSRG  1200
SSESKPKKIG KKRSSNASFA RVASEEDVQE DVQEDEEAEN EEEECTGYQC DMEGCTMSFT  1260
SEKQLALHKR NICPVRGCGK SFFSHKYLVQ HQRVHSDDRP LKCPWKGCKM TFKWAWSRTE  1320
HIRVHTGARP YVCAEPDCGQ TFRFVSDFSR HKRKTGHSVK KTKKR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A1e-771245136520140Lysine-specific demethylase REF6
6a58_A1e-771245136520140Lysine-specific demethylase REF6
6a59_A1e-771245136520140Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1943955KRKVRAKAVPRKK
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
Cis-element ? help Back to Top
SourceLink
PlantRegMapCsa06g022210.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY6644990.0AY664499.1 Arabidopsis thaliana relative of early flowering 6 (REF6) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010515159.10.0PREDICTED: lysine-specific demethylase REF6-like
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLR0FN140.0R0FN14_9BRAS; Uncharacterized protein
STRINGXP_010515159.10.0(Camelina sativa)
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]