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 KFK34138.1
Organism
Arabis alpina
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Arabideae; Arabis
Family C2H2
Protein Properties Length: 1378aa    MW: 154855 Da    PI: 8.5672
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
KFK34138.1genomeMPIPBRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.50.0004512611286123
                  EEET..TTTEEESSHHHHHHHHHH.T CS
     zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                  ++C    C++sF++  +L +H r+ +
  KFK34138.1 1261 FQCDleGCTMSFNSEKELAVHKRNiC 1286
                  89********************9877 PP
2zf-C2H211.80.0007712861308323
                  ET..TTTEEESSHHHHHHHHHHT CS
     zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                  Cp   Cgk F ++ +L +H r+H
  KFK34138.1 1286 CPvkGCGKNFFSHKYLLQHRRVH 1308
                  9999*****************99 PP
3zf-C2H2120.0006713441370123
                  EEET..TTTEEESSHHHHHHHHHH..T CS
     zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                  y+C    Cg++F+  s++ rH r+  H
  KFK34138.1 1344 YVCAepGCGQTFRFVSDFSRHKRKtgH 1370
                  899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.0E-151960IPR003349JmjN domain
PROSITE profilePS5118313.7862061IPR003349JmjN domain
PfamPF023757.8E-142154IPR003349JmjN domain
SMARTSM005582.2E-51200369IPR003347JmjC domain
PROSITE profilePS5118433.823203369IPR003347JmjC domain
SuperFamilySSF511974.39E-27218387No hitNo description
PfamPF023731.7E-37234352IPR003347JmjC domain
SMARTSM003551212611283IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.90212841313IPR007087Zinc finger, C2H2
SMARTSM003550.0212841308IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.609.2E-612861312IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012861308IPR007087Zinc finger, C2H2
SuperFamilySSF576676.97E-1013001342No hitNo description
Gene3DG3DSA:3.30.160.609.8E-913131337IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.92813141343IPR007087Zinc finger, C2H2
SMARTSM003550.001513141338IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013161338IPR007087Zinc finger, C2H2
SuperFamilySSF576673.04E-813321366No hitNo description
Gene3DG3DSA:3.30.160.601.8E-913381367IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.03213441375IPR007087Zinc finger, C2H2
SMARTSM003550.6213441370IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013461370IPR007087Zinc 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: 1378 aa     Download sequence    Send to blast
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASRYGIC KILPPVPPPS  60
KKTAISNLNR SLAARAAARV RDGGGSAFDY DGGPTFATRQ QQIGFCPRKQ RPVQRPVWQS  120
GEHYSFGEFE YKAKTFEKNY LKKCSKKSQL SALEMETLYW KATVDKPFSV EYANDMPGSA  180
FIPLSLAAAR RREYGGDGGT VGETAWNMRA MARAEGSLLK FMKEEIPGVT SPMIYIAMMF  240
SWFAWHVEDH DLHSLNYLHM GASKTWYGVP KDAAVAFEEV VRVHGYGGEL NPLVTFSTLG  300
EKTTVMSPEV FVKAGIPCCR LVQNPGDFVV TFPRAYHSGF SHGFNCGEAS NIATPEWLRM  360
AKDAAIRRAA ISYRPIVSHL QLLYDFALAL GSRVPTSIHT KPRSSRLKDK KRSEGEKLTK  420
ELFVQNIIHN NELLHSLGKG SPIALLPQSS SDKSVCSDQR KSLHLYXXXX MVSLSNGVKD  480
TVSVKEKFTS LCERNRNHLE KETQGTLTDA ERRKNVRLSD QRLFSCVTCG ILSFDCVAIV  540
QPKEAAARYL MSADCSFFND WTVASGSANL GQVARSLHPH CSFFNDWTVA SGSANLGQVA  600
RSLHPQSMEK HDADYFYDVP IEIMDQRTSS TSLTKAQKDN DALGLLASAY GDSSDSEEED  660
HKGIDIPISE GAFKASSVDT DGKEEARDGR SSDFNSQRLS CGKGKEVEVS HATSTCSTLS  720
CTSKQNKLSK GDNTSLVEIA LPFVPRSDDD SSRLHVFCLE HAAEVEEQLR PIGGIHIMLL  780
CHPEYPRIEA EAKIVAEELG VNQEWNDTEF RNVTQEDEET IQAALDNVGT KAGNSDWAVK  840
LGINLSYSAI LSRSPLYSKQ MPYNSIIYNA FGRSSPATSS PSKLEISGKR SSRQRKYVVG  900
KWCGKVWMSH QVHPFLLQQD LEGEESDRSH HLRVALDEDV TGKRLFPGNN SRDATTMFGR  960
KYSRKRKMRA KAVPRKKLTS FKREDGVSDD TSEDHSYKQQ WRASDNEEES YFEIGNTGSG  1020
DSSNHMSDHQ QLKGSRRHKG LKEFESGDEA SDRSLGEEYA VRDYAVSESS MENSFELYRE  1080
KQSRYDHEDD DLYRYPRGIP RNKRAKVFRN PVSYDSEENG AYQQRRRVST SKQARRMGGE  1140
YDSAENSLEE QNFSVTGKRQ TRSTAKRKAK IEAVQSPSDT EGCGLQGFAS GKKNRELDSY  1200
MEGPSTRLRV RNLKPSRGSK VTKPKKTGRK GISIATFSRA ASEEELEEDE GENEEEERTA  1260
FQCDLEGCTM SFNSEKELAV HKRNICPVKG CGKNFFSHKY LLQHRRVHSD DRPLKCPWKG  1320
CKMTFKWAWS RTEHIRVHTG ARPYVCAEPG CGQTFRFVSD FSRHKRKTGH SVKKTKKR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A4e-741260137822140Lysine-specific demethylase REF6
6a58_A4e-741260137822140Lysine-specific demethylase REF6
6a59_A4e-741260137822140Lysine-specific demethylase REF6
6ip0_A4e-7394654421Transcription factor jumonji (Jmj) family protein
6ip4_A4e-7394654421Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1962967SRKRKM
2964976KRKMRAKAVPRKK
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
PlantRegMapKFK34138.1
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_006404261.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A087GW860.0A0A087GW86_ARAAL; Uncharacterized protein
STRINGA0A087GW860.0(Arabis alpina)
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]