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 Carubv10016578m
Common NameCARUB_v10016578mg
Organism
Capsella rubella
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family C2H2
Protein Properties Length: 1398aa    MW: 156756 Da    PI: 7.4067
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10016578mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.90.0006812801305123
                       EEET..TTTEEESSHHHHHHHHHH.T CS
          zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                       y+C    C++sF++  +L  H r+ +
  Carubv10016578m 1280 YQCDmeGCTMSFNTEKQLALHKRNiC 1305
                       99********************9877 PP
2zf-C2H215.16.9e-0513051327323
                       ET..TTTEEESSHHHHHHHHHHT CS
          zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                       Cp   Cgk F ++ +L++H+r+H
  Carubv10016578m 1305 CPvkGCGKNFFSHKYLVQHQRVH 1327
                       9999*****************99 PP
3zf-C2H211.90.0006813631389123
                       EEET..TTTEEESSHHHHHHHHHH..T CS
          zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                       y+C    Cg++F+  s++ rH r+  H
  Carubv10016578m 1363 YVCAepGCGQTFRFVSDFSRHKRKtgH 1389
                       899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005456.6E-161960IPR003349JmjN domain
PROSITE profilePS5118313.912061IPR003349JmjN domain
PfamPF023755.8E-142154IPR003349JmjN domain
SMARTSM005582.3E-53200369IPR003347JmjC domain
PROSITE profilePS5118434.846203369IPR003347JmjC domain
SuperFamilySSF511973.57E-28216387No hitNo description
PfamPF023732.1E-38233352IPR003347JmjC domain
SMARTSM003559.112801302IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.17313031332IPR007087Zinc finger, C2H2
SMARTSM003550.0113031327IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.2E-613041331IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028013051327IPR007087Zinc finger, C2H2
SuperFamilySSF576673.82E-1013191361No hitNo description
Gene3DG3DSA:3.30.160.609.9E-913321356IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.92813331362IPR007087Zinc finger, C2H2
SMARTSM003550.001513331357IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013351357IPR007087Zinc finger, C2H2
SuperFamilySSF576673.14E-813511385No hitNo description
Gene3DG3DSA:3.30.160.601.8E-913571386IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.03213631394IPR007087Zinc finger, C2H2
SMARTSM003550.6213631389IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013651389IPR007087Zinc 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: 1398 aa     Download sequence    Send to blast
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASKYGIC KILPPVPPPS  60
KKTSISNLNR SLAARAAARV RDGGFGACDY DGGPTFATRQ QQIGFCPRKQ RPVQRPVWQS  120
GEEYSFGEFE FKAKSFEKAY LKKCGKKSQL SALEIETLYW RATVDKPFSV EYANDMPGSA  180
FIPLSLAAAR RRESGGDGGT VGETAWNMRA MARAEGSLLK FMKEDIPGVT SPMVYIAMMF  240
SWFAWHVEDH DLHSLNYLHM GASKTWYGVP KEAAPAFEEV VRVHGYGGEL NPLVTFSTLG  300
EKTTVMSPEV FVKAGIPCCR LVQNPGEFVV TFPGAYHSGF SHGFNFGEAS NIATPQWLRM  360
AKDAAIRRAA INYPPMVSHL QLLYDFALAL GSRVPTSINA KPRSSRLKDK KRSEGERLTK  420
KLFVDNIIRN NELLYSLGKG SPVALLPQSS SDISVCSDLR IGSDLRTNQE SPIQLKSEDL  480
SCDSVMVGLN NGLKDTVSVK EKFTSLCERN RNHLASRGKE TQETLSDTEG RNNAGAVGLS  540
DQRLFSCVTC GVLSFDCVGI VQPKEASAGY IMSANSSFFN DWTAASGSAN RGQDARSLHL  600
RKFQIALPFN CCFLAFILTL FHHAESTEKD DVNYFSNVPV QTGHQRTLTT SLTNAHKDNG  660
ALGLLASAYG DSSDSEEDDN KGFDASNLEG ERKKYDQESA CAFKASSFDT DGNEEARDGQ  720
TSDFNSQRLT SKQNSLSKCG ISSLLEITLP FIPRSDDDPC RLHVFCLEHA AEVEQQLRSI  780
GGIHIMLLCH PEYPRIEAEA KIVAEEFAIN HEWNDTEFRN VTREDEETIQ AALDNVEAKG  840
GNSDWTVKLG INLSYSAFLS RSPLYSKQMP YNSVIYNVFG RSSTAVSSLS KPEVSGRRSS  900
RQRKYVVGKW CGKVWMSHQV HPFLLEEDLE GEESERSCPL RAAMDEDVTG KRLFSCNVSR  960
DAATMFGRKY CRKRKIRAKA VPRKKLTAFK REDGVSDDTS EDHSYKQQWR ASGNEEESYF  1020
ETGHTASGDS SNQMSDQGKE IVRHKGYNGF ESDDEVSDRS LGEEYTVREC AVSESSMENG  1080
FQPYREKQAM YDDNDDDGDD DDDDDMYRHP RGIPRSKRSK VIRNPVSYDS EENDVYQQRG  1140
RRVSRSSRQA NRMGGEYDSA ENSFEELDFC TTGKRQTRST AKRKAKTETV QSPRDTKGRS  1200
LQEFASGKKI EELDSYMEGP STRLRLRNQK PSRGSFESKP KKVGKKRSSN ASFSRAASEE  1260
YVQEDEEAEA ENEEEECTGY QCDMEGCTMS FNTEKQLALH KRNICPVKGC GKNFFSHKYL  1320
VQHQRVHSDD RPLKCPWKGC KMTFKWAWSR TEHIRVHTGA RPYVCAEPGC GQTFRFVSDF  1380
SRHKRKTGHS VKKTKKR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A5e-771277139720140Lysine-specific demethylase REF6
6a58_A5e-771277139720140Lysine-specific demethylase REF6
6a59_A5e-771277139720140Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1972984KRKIRAKAVPRKK
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
PlantRegMapCarubv10016578m
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_023637886.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLR0FN140.0R0FN14_9BRAS; Uncharacterized protein
STRINGXP_006290503.10.0(Capsella rubella)
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]