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 Vradi05g05790.1
Organism
Vigna radiata
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: 1639aa    MW: 184361 Da    PI: 8.858
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Vradi05g05790.1genomeSNUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H210.90.001415221547123
                       EEET..TTTEEESSHHHHHHHHHH.T CS
          zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                       y+C    C++sF +k +L +H r+ +
  Vradi05g05790.1 1522 YQCDmdGCSMSFGSKQELLHHKRNiC 1547
                       99********************9877 PP
2zf-C2H212.80.0003715471569323
                       ET..TTTEEESSHHHHHHHHHHT CS
          zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                       Cp   Cgk F ++ +L++H r+H
  Vradi05g05790.1 1547 CPvkGCGKKFFSHKYLVQHRRVH 1569
                       9999*****************99 PP
3zf-C2H211.70.0008116051631123
                       EEET..TTTEEESSHHHHHHHHHH..T CS
          zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                       y+C    Cg++F+  s++ rH r+  H
  Vradi05g05790.1 1605 YVCAepGCGQTFRFVSDFSRHKRKtgH 1631
                       899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005452.2E-163071IPR003349JmjN domain
PROSITE profilePS5118314.6033172IPR003349JmjN domain
PfamPF023753.7E-143265IPR003349JmjN domain
PROSITE profilePS5118433.744192361IPR003347JmjC domain
SMARTSM005589.3E-49192361IPR003347JmjC domain
SuperFamilySSF511975.22E-26192379No hitNo description
PfamPF023731.8E-35225344IPR003347JmjC domain
SMARTSM003557.115221544IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.94415451574IPR007087Zinc finger, C2H2
SMARTSM003550.004515451569IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.4E-615461573IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028015471569IPR007087Zinc finger, C2H2
SuperFamilySSF576672.31E-915611603No hitNo description
Gene3DG3DSA:3.30.160.601.2E-815741599IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001415751599IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.74115751604IPR007087Zinc finger, C2H2
PROSITE patternPS00028015771599IPR007087Zinc finger, C2H2
SuperFamilySSF576674.19E-815931627No hitNo description
Gene3DG3DSA:3.30.160.602.5E-916001628IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.6216051631IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.46816051636IPR007087Zinc finger, C2H2
PROSITE patternPS00028016071631IPR007087Zinc 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: 1639 aa     Download sequence    Send to blast
MRATEKKSGI MGGGSEGSAD VLPWLKSMPV APEYRPTAAE FQDPIGYIFK IEKEASKYGI  60
CKIIPPFPPS PKKTAIANLN RSLAVSGSTF TTRQQQIGFC PRRPRPVQRP VWQSGDHYTF  120
TEFEFKAKSF EKAYLKRHTR KGPSPGPGLT PLETETLFWK ATLDKPFSVE YANDMPGSAF  180
SPKCRHTGDP TSLADTPWNM RAVSRATGSL LRFMKEEIPG VTSPMVYVAM LFSWFAWHVE  240
DHDLHSLNYL HMGAGKTWYG VPRDAAVAFE EVVRVHGYGG EINPLVTFAI LGEKTTVMSP  300
EVFLSAGVPC CRLVQNAGEF VVTFPRAYHT GFSHGFNCGE AANIATPEWL RVAKDAAIRR  360
ASLNYPPMVS HFQLLYDLAL ALCSRIPASI SAEPRSSRLK DKKKGEGETV IKELFVQDVL  420
QNNDLLHILG KESAVVLLPR SSVDISVCSK LRVGSQQSIN VSNSEGMHSS KDFVSDDLVF  480
NRSHGIKQEK TFYSVKDKFS TMYERNRVSS FDVNGSLISS SSKPLQRDTE GGTSKEDGLS  540
DQRLFSCVTC GILSFSCVAI VQPRDPAARY LVSADCSFCN DWVVGSGVSN SKLTTAPEKA  600
IIPVPNMYTG SFSYGPIGVY WGPKGWMKKN VQDGMQDVSV QSSRYASSIE SEKGNTALAL  660
LASAYGNSSD SEEDQISVDG HETNVLTSAS ESLLSHTQDS HASPVAALDS GDNITLMSAS  720
CEGLMHRRFE GNLSHQSLDH SLKKQDYNIT SGVTFENMKT VPNSTSNCSQ DANDAERSLS  780
KMSMVPFDNK NASMVLQSDE DSSRMHVFCL EHAAEAEKQL RPIGGAHIFL LCHPDILNWL  840
RNKGTVAMKN ESVVMEVMSV YVQCKKSSSP NAKVKFNYPK IEAEAKVVAE DLGIDYTWKS  900
IAYRHASKED EERIQLALDS EEAIPGNGDW AVKLGINLFY SAHLSRSPLY SKQMPYNSVI  960
YCAFGCSSPA SSSEEPKVYQ RRVNRQKKVV AGKWCGKVWM SNQVHPLLAK RDSEDAEDEK  1020
ILLGWISPEE RIERSESTPK GETTSRKSGK KRKSTAENGR TRKGSYAKKN VVSYNSIEDK  1080
PNSQPRSVHR SKKARNVGRD RAALKGDTSA YNHRKPISKE TNFTESDAVS DDSLDDEDDH  1140
MQHGRNFDID NHVVSDDTGD CDSDWQQREE HSSKDDEDME RDAISEDSEG KHDKFISEED  1200
IISDDQMESC FQKRQRRTPK SRQAKYLTGK SIISNDQLEL KMQKQQRRNP QSRQAKYLDE  1260
EDIASDDQLE GHYRRYQRRN PKGRQAKCVV EEDEMSGDQL EDHCQKLQTS FSRKKQNKGI  1320
NREDKYVMSD DQLEDHFPKQ QRRIPKSRQN RYPDKEVMDD SAENNTRLLH RTPKRKQAKC  1380
MDEDDLNSDD EMEDDQKLRR TLRSKQSKPK TLQQMKQANS VHAKNQASRS IKRGSRVLVK  1440
SKTPQQIKPR NKQSTNSREF SLLVEDEEEG GPSTRLRKRA TKAQGTEGKL KEKQTKRKKV  1500
KNDSTAKVSV GHVKGKDEEA DYQCDMDGCS MSFGSKQELL HHKRNICPVK GCGKKFFSHK  1560
YLVQHRRVHE DERPLKCPWK GCKMTFKWAW ARTEHIRVHT GARPYVCAEP GCGQTFRFVS  1620
DFSRHKRKTG HSAKKSRQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A2e-79203824353Transcription factor jumonji (Jmj) family protein
6ip4_A2e-79203824353Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
114761498RKRATKAQGTEGKLKEKQTKRKK
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
PlantRegMapVradi05g05790.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
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_014501175.10.0lysine-specific demethylase JMJ705
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A1S3U5790.0A0A1S3U579_VIGRR; lysine-specific demethylase JMJ705
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]