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 Csa04g033550.1
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: 1444aa    MW: 162651 Da    PI: 8.1825
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Csa04g033550.1genomeCSGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.40.00113261351123
                      EEET..TTTEEESSHHHHHHHHHH.T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                      y+C    C++sF++  +L  H r+ +
  Csa04g033550.1 1326 YQCDmeGCTMSFTSEKQLALHKRNiC 1351
                      99********************9877 PP
2zf-C2H216.81.9e-0513511373323
                      ET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                      Cp   CgksF ++ +L++H+r+H
  Csa04g033550.1 1351 CPvrGCGKSFFSHKYLVQHQRVH 1373
                      9999*****************99 PP
3zf-C2H211.90.000714091435123
                      EEET..TTTEEESSHHHHHHHHHH..T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                      y+C    Cg++F+  s++ rH r+  H
  Csa04g033550.1 1409 YVCAepGCGQTFRFVSDFSRHKRKtgH 1435
                      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
PfamPF023756.0E-142154IPR003349JmjN domain
SMARTSM005581.5E-53200369IPR003347JmjC domain
PROSITE profilePS5118434.854203369IPR003347JmjC domain
SuperFamilySSF511972.53E-28215388No hitNo description
PfamPF023732.2E-38233352IPR003347JmjC domain
SMARTSM003558.513261348IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.42213491378IPR007087Zinc finger, C2H2
SMARTSM003550.001813491373IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.606.3E-713501377IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028013511373IPR007087Zinc finger, C2H2
SuperFamilySSF576674.17E-1013651407No hitNo description
Gene3DG3DSA:3.30.160.601.0E-813781402IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.92813791408IPR007087Zinc finger, C2H2
SMARTSM003550.001513791403IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013811403IPR007087Zinc finger, C2H2
SuperFamilySSF576673.24E-813971431No hitNo description
Gene3DG3DSA:3.30.160.601.8E-914031432IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.03214091440IPR007087Zinc finger, C2H2
SMARTSM003550.6214091435IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028014111435IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 1444 aa     Download sequence    Send to blast
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASKYGIC KILPPLPPPS  60
KKTSISNLNR SLAARAVGRV RDGGFGACDY DGGPTFATRQ QQIGFCPRKQ RPVQRPVWQS  120
GEEYSFGEFE FKARSFEKNY LKKCGKKSQL SPLEIETLYW RASVDKPFSV 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 GSRVPTSINT NPRSSRLKDK KRSEGERLTK  420
KLFVENIIRN NELLSSLGKG SPVALLPQSS SDISVCSDLR IGSDLTTNQD NPIQLKSEDF  480
SSDSVMVGLD NGLKDTVSVK EKFTSLCERN RNHLASRENE TQGTLSEAER REKGGAVWLS  540
DQRLFSCVTC GVLSFDCVAI IQPREAAARY IMSADSSFFN DRKAVSESAN LGQAARSHHP  600
QSMEKHDVDY FSNVSVQTGH QRTSTTSQTN AQKDNGSLGL LVSAYGDSSD SEEEDNRGLD  660
ASTSEGERKK YDQESAFKAS SFDTDDNEVA RDGRTSDFNS QSLIGKQNSL SKGDNSSLLD  720
ITLPFVPRSD EDPCRLHVFC LEHAAEVEQQ LRAIGGIHIM LLCHPEYRRI EAEAKIVAEE  780
LAINHEWNDT EFRNVTREDE ETIQAALDNV EAKGGNSDWT VKLAINLSYS AILSHSPLYS  840
KQMPYNSVIY NVFGRSSPAI SSLSKPEVSG KRSSRQRKYV VGKWCGKVWM SHQVHPFLLE  900
DLEGEEERSC HLRTAMDEDV TGKRLFPCNV SRDAATMFGR KYCRKRKVRA KAVPRKKLTS  960
FKREDGVSDD TSEDHSYKQQ WRASGNEEES YFETGHTASG DSSNQMSDQR KEIVRHKATM  1020
FGRKYCRKRK VRAKAVPRKK LTSFKREDGV SDDTSEDHSY KQQWRASGNE EESYFETGHT  1080
ASGDSSNQMS DQRKEIVRHK GYNVFKSDDE VSDRSLGEEY SVRECAVSES SMENGFQPYR  1140
EKQSMYDRDD DDDDMYKHPR EIPRSKRTKV FRNPVSYDSE ENGVYQQRGR VSRSSRQANR  1200
MGGEYDSAEN SFEELDFCST GKRQTRSTAK RKAKTKSVQS PRDAKGRTLQ EFASGMKTEE  1260
LDSFMEGPST RLRMRNQKPS RGSSESKPKK IGKKRSSNAS FARVASEEDV QEDEEAENEE  1320
EECTGYQCDM EGCTMSFTSE KQLALHKRNI CPVRGCGKSF FSHKYLVQHQ RVHSDDRPLK  1380
CPWKGCKMTF KWAWSRTEHI RVHTGARPYV CAEPGCGQTF RFVSDFSRHK RKTGHSVKKT  1440
KKR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A2e-761323144320140Lysine-specific demethylase REF6
6a58_A2e-761323144320140Lysine-specific demethylase REF6
6a59_A2e-761323144320140Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
110271039KRKVRAKAVPRKK
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCsa04g033550.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
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_010503472.10.0PREDICTED: lysine-specific demethylase REF6-like
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLD7LRW50.0D7LRW5_ARALL; Uncharacterized protein
STRINGXP_010503472.10.0(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]