PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Thhalv10010068m
Common NameEUTSA_v10010068mg
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Eutremeae; Eutrema
Family C2H2
Protein Properties Length: 1365aa    MW: 154111 Da    PI: 8.0399
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thhalv10010068mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H215.16.7e-0512721294323
                       ET..TTTEEESSHHHHHHHHHHT CS
          zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                       Cp   Cgk F ++ +L++H+r+H
  Thhalv10010068m 1272 CPvkGCGKNFFSHKYLVQHQRVH 1294
                       9999*****************99 PP

2zf-C2H210.80.001613301356123
                       EEET..TTTEEESSHHHHHHHHHH..T CS
          zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                       y+C    C+++F+  s++ rH r+  H
  Thhalv10010068m 1330 YVCAepGCDQTFRFVSDFSRHKRKtgH 1356
                       899999****************99666 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005453.4E-161960IPR003349JmjN domain
PROSITE profilePS5118314.0772061IPR003349JmjN domain
PfamPF023751.0E-142154IPR003349JmjN domain
SMARTSM005581.1E-50199368IPR003347JmjC domain
PROSITE profilePS5118433.062202368IPR003347JmjC domain
SuperFamilySSF511972.5E-26214386No hitNo description
PfamPF023731.9E-37232351IPR003347JmjC domain
SMARTSM003551112471269IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.17312701299IPR007087Zinc finger, C2H2
SMARTSM003550.0112701294IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.2E-612711293IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012721294IPR007087Zinc finger, C2H2
SuperFamilySSF576674.03E-1012861328No hitNo description
Gene3DG3DSA:3.30.160.603.0E-912941320IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.92813001329IPR007087Zinc finger, C2H2
SMARTSM003550.001513001324IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013021324IPR007087Zinc finger, C2H2
SuperFamilySSF576675.87E-813181352No hitNo description
Gene3DG3DSA:3.30.160.604.7E-913211353IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.24213301361IPR007087Zinc finger, C2H2
SMARTSM003550.913301356IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013321356IPR007087Zinc 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: 1365 aa     Download sequence    Send to blast
MVVSEQSPDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASRYGIC KIVPPVPPPS  60
KKTTISNLNR SLASLATARV RDGGDAFDYD GAPTFATRQQ QIGFCPRKQR PVQRPVWQSG  120
EHYSFGEFEF KAKNFEKNYL RKCGKKSQLS ALEIETLYWR ATVDKPFSVE YANDMPGSAF  180
IPLSLAAARR RESGGDGGTV GETAWNMRAM ARAEGSLLKF MKEEIPGVTS PMVYIAMMFS  240
WFAWHVEDHD LHSLNYLHMG ASKTWYGVPK DAAVAFEEVV RVHGYGGELN PLVTFSTLGD  300
KTTVMSPEVF VKAGIPCCRL VQNPGEFVVT FPRAYHSGFS HGFNCGEASN IATPEWLRIA  360
KDAAIRRAAI NYPPMVSHLQ LLYDFALALC SRVPTSIHTK PRSSRLKDKK RSEGEKLTKE  420
LFVQNIIHNN ELLRSLGKRS PVALLPQSSS DVSVCSDLRV GSHLRTNQER PIQLKSEDFS  480
SDSIMAGLSN GFKDVVSVKE KFTSLCERNR NYLASRENET QGTLTDAERK NDRAVGLSDQ  540
RLFSCVTCGI LCFDCVAIVQ PKEAAARYLM SADCSFFNDW TATSGSANLG QDSRFSAVKP  600
HSESTGKHDV DDFYNVPVQT TDERTSTTSL TKAQKEDGAL GLLASAYGDS SDSEEEDHKG  660
LDTIISEERK YDHNGIEEAT DGQAFDNSSQ RLSCGKGKGV VEGSNAAEHD RLSNGGSTSN  720
LEIAFPFVPR SDDDSSRLHV FCLEHAAEVE QQLRPLGGIR IMLLCHPEYP RIEAEAKIVA  780
DELGVNHEWN DTEFRNVTRE DEEMIQAALD NVEAKAGNSD WSVKLGINLS YSAILSRSPL  840
YSKQMPYNSV IYNAFGRGSP ATSSPTKPQV SGKRSSRQRK YVVGKWCGKV WMSHQVHPFL  900
LQQDLEGDES ERSCHLRGAL DDDVTGKRLS PCDVSRDATT MFGRKYCRKR KMRAKAVPRK  960
KLTSFKREDG VSDDTSEDHS YKQQWRASRN EEESYFETGN TVSGDSSNEM SDSQLKRIRR  1020
DKGVKEFESD DEVSDRSLGE EYAVRECAVS ESSMENNFQP YKQSVDRKPL EDTVYGHNDD  1080
IIYRYPRGIP RSKRKKVFRN PVSYDSEEND IYQQRRNIQA TGEYVSAEDS LEEQDFYTTG  1140
KRQTRSTAKR KVKTEIVQSR RDTRCRTLQQ SGSGKMNQEL NSYMEGPSTR LRVRNQNPSR  1200
GFSETKPKKT SKKRRSNASF SRIVSEEELE EEDKEEVENE EEECAAYRCD MEGCRMSFNS  1260
EKQLSLHKRN ICPVKGCGKN FFSHKYLVQH QRVHSDDRPL KCPWKGCKMT FKWAWSRTEH  1320
IRVHTGARPY VCAEPGCDQT FRFVSDFSRH KRKTGHSVKK AKRR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A5e-751244136420140Lysine-specific demethylase REF6
6a58_A5e-751244136420140Lysine-specific demethylase REF6
6a59_A5e-751244136420140Lysine-specific demethylase REF6
6ip0_A5e-7394564413Transcription factor jumonji (Jmj) family protein
6ip4_A5e-7394564413Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1948960KRKMRAKAVPRKK
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
PlantRegMapThhalv10010068m
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_006404260.10.0lysine-specific demethylase REF6
RefseqXP_024013589.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLV4M0K30.0V4M0K3_EUTSA; Uncharacterized protein
STRINGXP_006404260.10.0(Eutrema salsugineum)
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]