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 Vang0052ss00070.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna
Family C2H2
Protein Properties Length: 1664aa    MW: 187239 Da    PI: 8.6814
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Vang0052ss00070.1genomeSNUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.80.0003615721594323
                         ET..TTTEEESSHHHHHHHHHHT CS
            zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                         Cp   Cgk F ++ +L++H r+H
  Vang0052ss00070.1 1572 CPvkGCGKKFFSHKYLVQHRRVH 1594
                         9999*****************99 PP

2zf-C2H211.70.0008216301656123
                         EEET..TTTEEESSHHHHHHHHHH..T CS
            zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                         y+C    Cg++F+  s++ rH r+  H
  Vang0052ss00070.1 1630 YVCAepGCGQTFRFVSDFSRHKRKtgH 1656
                         899999****************99666 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005452.2E-165596IPR003349JmjN domain
PROSITE profilePS5118314.6035697IPR003349JmjN domain
PfamPF023753.8E-145790IPR003349JmjN domain
SuperFamilySSF511972.66E-26217404No hitNo description
PROSITE profilePS5118434.037217386IPR003347JmjC domain
SMARTSM005586.9E-49217386IPR003347JmjC domain
PfamPF023731.6E-35250369IPR003347JmjC domain
SMARTSM003556.515471569IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.94415701599IPR007087Zinc finger, C2H2
SMARTSM003550.004515701594IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.604.0E-615711598IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576674.63E-615711603No hitNo description
PROSITE patternPS00028015721594IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.3E-815991624IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.74116001629IPR007087Zinc finger, C2H2
SMARTSM003550.001416001624IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028016021624IPR007087Zinc finger, C2H2
SuperFamilySSF576672.73E-916101654No hitNo description
Gene3DG3DSA:3.30.160.602.5E-916251653IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.46816301661IPR007087Zinc finger, C2H2
SMARTSM003550.6216301656IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028016321656IPR007087Zinc 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: 1664 aa     Download sequence    Send to blast
MAEKFPSSGN RGRDANTRCE LAEASMRATE KKSGIMGGGS EGSADVLPWL KSMPVAPEYR  60
PTAAEFQDPI GYIFKIEKEA SKYGICKIIP PFPPSPKKTA IANLNRSLAV SGSTFTTRQQ  120
QIGFCPRRPR PVQRPVWQSG DHYTFTEFEF KAKSFEKAYL KRHTRKGPSP GPGLTPLETE  180
TLFWKATLDK PFSVEYANDM PGSAFSPKCR HTGDPTSLAD TPWNMRVVSR ATGSLLRFMK  240
EEIPGVTSPM VYVAMLFSWF AWHVEDHDLH SLNYLHMGAG KTWYGIPRDA AVAFEEVVRV  300
HGYGGEINPL VTFAILGEKT TVMSPEVFLS AGVPCCRLVQ NAGEFVVTFP RAYHTGFSHG  360
FNCGEAANIA TPEWLRVAKD AAIRRASLNY PPMVSHFQLL YDLALALCSR IPASISAEPR  420
SSRLKDKKKG EGETVIKELF VQDVLQNNDL LHILGKGSAV VLLPRSSVDI SVCAKLRVGS  480
QQSINVSNSE GMHSSKDFVS DDLVFNRSHG IKQEKTFYSV KDKFSMIYER NRVSSFDVNG  540
SLSTSSSKPL QRDTEGETSK EDGLSDQRLF SCVTCGILSF SCVAIVQPRD PAARYLMSAD  600
CSFFNDWVVG SGVSNSKLTT APEEATIPVP NMYTGSFSYG PIGVYWGPKG WMKKNVQDGM  660
QDVSVQSSRY ALSIESEKGN TALALLASAY GNSSDSEEDQ ISVDDHETNV LISASESLLS  720
HTQDSHASPV SALDSGDNIT LMSTSCEGLM HRRFEGNLSH QSLDHSLKKQ DYNITSGVTF  780
ENMKTVPTST SNCSQDANDA ERSLCKMSMV PFDNKNASMV LQSDEDSSRM HVFCLEHAAE  840
AEKQLRPIGG AHIFLLCHPD ILNWLRNKGT VAMKNESVVM EVISVYVQCK ESSSPNAKVK  900
FNYPKIEAEA KLVAEDLGID YTWKSIAYRH ASKEDEERIQ SALDSEEAIP GNGDWAVKLG  960
INLFYSAHLS RSPLYSKQMP YNSVIYCAFG CSSPASSPEE PKVYQRRVNR QKKVVAGKWC  1020
GKVWMSNQVH PLLAKRDSED AEDEKILLGW ILPEERIERS ESTPKGETTS RKSGKKRKST  1080
AENGRTRKVS YAKKNVVSYN STEDKPNSQP RSVHRSKKAR NVGRDRTALK GDTSAYNHRK  1140
PISKQTNFTE SDAVSDDSLD DEDDHMQHGR NFDIDNDVVS DDTGDCDSDW QQREEHSSKD  1200
DEDMERDAIS EDSEGKHDKF ISEEDIISDD QMESCFQKRQ RRTPKSRQAK YLTGKSIISD  1260
DQLELKMQKQ QRRNPKSRQA KYLNEEDIAS DDQLEGHYRR YQRRNPKGRQ AKCVAEEDEM  1320
SGDQLEDHCQ KLQTSFSRKK QNKGINREDK YVMSDDQLED HFPKQQRRIP KSRQNKYLDK  1380
EVMDDSAENN SRLLHRTPKR KQAKCMDEDD LNSDDEMEDD QKLRRTLRSK QSKPKTLQQM  1440
KQANSVHAKN QASRSIKRGS RVLVKSKTPQ QIKPRNKQSS NSREFSLLME DEEEGGPSTR  1500
LRKRATKAQG TEGKLKEKQT KRKKVKNDST GKVSVGHVKG KEEEADYQCD IDGCSMSFGS  1560
KQELLHHKKN ICPVKGCGKK FFSHKYLVQH RRVHEDERPL KCPWKGCKMT FKWAWARTEH  1620
IRVHTGARPY VCAEPGCGQT FRFVSDFSRH KRKTGHSAKK SRQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A2e-79454074353Transcription factor jumonji (Jmj) family protein
6ip4_A2e-79454074353Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
115011523RKRATKAQGTEGKLKEKQTKRKK
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
PlantRegMapVang0052ss00070.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0150350.0AP015035.1 Vigna angularis var. angularis DNA, chromosome 2, almost complete sequence, cultivar: Shumari.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_017421723.10.0PREDICTED: lysine-specific demethylase REF6-like
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A0L9UCP50.0A0A0L9UCP5_PHAAN; Uncharacterized protein
TrEMBLA0A0S3RFS40.0A0A0S3RFS4_PHAAN; Uncharacterized protein
STRINGXP_007137965.10.0(Phaseolus vulgaris)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF56483250
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]