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 XP_010550712.1
Organism
Tarenaya hassleriana
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Cleomaceae; Tarenaya
Family C2H2
Protein Properties Length: 1489aa    MW: 168570 Da    PI: 8.119
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_010550712.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H214.69.3e-0513731398123
                      EEET..TTTEEESSHHHHHHHHHH.T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                      y+C+   C++sFs+k +L  H r+ +
  XP_010550712.1 1373 YRCNmeGCTMSFSTKQQLALHKRNiC 1398
                      99********************9877 PP
2zf-C2H212.50.0004413981420323
                      ET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                      Cp   Cgk F ++ +L++H r+H
  XP_010550712.1 1398 CPvkGCGKKFFSHKYLVQHKRVH 1420
                      9999*****************99 PP
3zf-C2H211.80.0007314561482123
                      EEET..TTTEEESSHHHHHHHHHH..T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                      y+C    Cg++F+  s++ rH r+  H
  XP_010550712.1 1456 YVCAepGCGQTFRFVSDFSRHKRKtgH 1482
                      899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005456.0E-151960IPR003349JmjN domain
PROSITE profilePS5118313.8832061IPR003349JmjN domain
PfamPF023752.2E-132154IPR003349JmjN domain
SuperFamilySSF511976.04E-28115176No hitNo description
PROSITE profilePS5118433.752196365IPR003347JmjC domain
SMARTSM005584.5E-52196365IPR003347JmjC domain
SuperFamilySSF511976.04E-28214384No hitNo description
PfamPF023731.2E-37229348IPR003347JmjC domain
SMARTSM003557.813731395IPR015880Zinc finger, C2H2-like
SuperFamilySSF576675.15E-613961432No hitNo description
PROSITE profilePS5015712.32113961425IPR007087Zinc finger, C2H2
SMARTSM003550.004613961420IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.8E-513971424IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028013981420IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.6E-914251450IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.61414261455IPR007087Zinc finger, C2H2
SMARTSM003550.001414261450IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028014281450IPR007087Zinc finger, C2H2
SuperFamilySSF576673.53E-1014361481No hitNo description
Gene3DG3DSA:3.30.160.601.8E-1014511479IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.6214561482IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.03214561487IPR007087Zinc finger, C2H2
PROSITE patternPS00028014581482IPR007087Zinc 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: 1489 aa     Download sequence    Send to blast
MAVSEASQDV FPWLKSLPLA PEFRPSPAEF QDPIAYIFKI EKEASKYGIC KILPPVPPAS  60
KKTMISNLNR SLAARAAAAA REGGACDYDR PTFTTRQQQI GFCARKQRPA QRPVWQSGEH  120
YTFQEFEAKA KNFEKNYLKK CGKKGPLSAL EIETLYWRAT VDKPFSVEYA NDMPGSAFIP  180
LSTAAVRRRE SGDGGTVGET TWNMRAVSRA EGSLLKFMKE EIPGVTSPMV YIAMMFSWFA  240
WHVEDHDLHS LNYLHMGAGK TWYGVPKDAA VAFEEVVRVH GYGGELNPLV TFATLGEKTT  300
VMSPEVFVKA GIPCCRLVQN PGEFVVTFPR AYHSGFSHGF NCGEASNIAT PEWLTMAKDA  360
AIRRAAINYP PMVSHFQLLY DFALALCSRV PASLTTKPRS SRLKDKKKSE GERLTKELFV  420
QNVIKNNKLL HSLGRGSLVV LLPRSSSDIS VCSDLRVGSQ LRTNQEKTLQ VFRDDVKPEE  480
LGSSYGMIGF NNDTKLDKGT VSVKEKFTSL CERNRNFPSW GNNTQGTLID ARRERGDRAE  540
GLSDQRLFSC VTCGILSFDC VAIVQPREAA ARYLMSADCS FFNDWTVGSG LASSGQDTSS  600
PVMKPVAQGT GKRDVNYLYD VPVQTGDCQM KTGNQRNGTA SKTNEEKDSG ALGLLASTYG  660
DSDSEEDNDD PDVPLSEGET NITNCSPPKK YLQDCVSQKM DCNEEAGLRQ SDLNFRTDQT  720
CDGTDEFRAQ RLACRRSNGV EVHATSSCST VSCTTEQKRL GLGEGTTSLL DMDLPFVPRS  780
NEDSSRLHVF CLEHAAEVEQ QLRPIGGVRI MLICHPEYPT IEAEAKLVAE ELEIDHQWND  840
VEFRSVTRED EGRIQSALDN EEAKAGNSDW AVKLGINLFY SAVLSRSPLY SKQMPYNSVI  900
YSAFGRSSPA SSPSKPEFPG RRSSRQKKFV VGKWCGKVWM SHQVHPFLVQ QDSEDEELDR  960
NFHSRAVMDE GVTERKPFSI LRNVTTMVAR KYCRKRKMRA KPMSRKKLTS FRTECGVSDD  1020
TSEDHPYKQQ WRASGNEEDS YFETGNTVSG DLSDQMSDQR LGRRGTKFQD EEDERSDDMS  1080
EDKYPNLKRK GILRHKGVHE FESEDEVSDR SLAEEYTARD FAPSDNSMEN GFQPNKQSRL  1140
LEMDREASDD DSADDDDDNI YRQQREIPRS KRTRIFKNVF SYDSEENGSY RHRSRMPRRT  1200
RKASRIGRKE EFSYESAEDN TDDENRRVMK HRKVKNIEEK EDERCSDSVE EQDFCSRRKR  1260
TATRKAKPEI LQSLKGTKGQ PASRKKKKKQ EGIRVLNVKQ EKDNVPLDSY TEGPSTRLRV  1320
RNQKPSRVSE TKSKKPGKKE RNASSFSRVA NEEDDDDAEE EEEDDEEEGS SVYRCNMEGC  1380
TMSFSTKQQL ALHKRNICPV KGCGKKFFSH KYLVQHKRVH LDDRPLKCPW KGCKMTFKWA  1440
WARTEHIRVH TGERPYVCAE PGCGQTFRFV SDFSRHKRKT GHSVKKTKR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A2e-7694534413Transcription factor jumonji (Jmj) family protein
6ip4_A2e-7694534413Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
19941006KRKMRAKPMSRKK
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
PlantRegMapXP_010550712.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010550712.10.0PREDICTED: lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A1J3JIY40.0A0A1J3JIY4_NOCCA; Lysine-specific demethylase REF6
STRINGXP_010550712.10.0(Tarenaya hassleriana)
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]