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 Phvul.009G169700.1
Common NamePHAVU_009G169700g
Organism
Phaseolus vulgaris
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; Phaseolus
Family C2H2
Protein Properties Length: 1597aa    MW: 179612 Da    PI: 8.5949
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Phvul.009G169700.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.50.0009514801505123
                          EEET..TTTEEESSHHHHHHHHHH.T CS
             zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                          y+C    C++sF +k +L +H r+ +
  Phvul.009G169700.1 1480 YQCDidGCSMSFGSKQELLHHKRNiC 1505
                          99********************9877 PP
2zf-C2H212.80.0003615051527323
                          ET..TTTEEESSHHHHHHHHHHT CS
             zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                          Cp   Cgk F ++ +L++H r+H
  Phvul.009G169700.1 1505 CPvkGCGKKFFSHKYLVQHRRVH 1527
                          9999*****************99 PP
3zf-C2H211.50.0009115631589123
                          EEET..TTTEEESSHHHHHHHHHH..T CS
             zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                          y+C    Cg++F+  s++ rH r+  H
  Phvul.009G169700.1 1563 YVCAeqGCGQTFRFVSDFSRHKRKtgH 1589
                          89********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005458.5E-183071IPR003349JmjN domain
PROSITE profilePS5118315.4763172IPR003349JmjN domain
PfamPF023753.5E-163265IPR003349JmjN domain
SuperFamilySSF511973.3E-26191381No hitNo description
SMARTSM005581.5E-48194363IPR003347JmjC domain
PROSITE profilePS5118433.744194363IPR003347JmjC domain
PfamPF023732.4E-35227346IPR003347JmjC domain
SMARTSM003555.914801502IPR015880Zinc finger, C2H2-like
SMARTSM003550.004515031527IPR015880Zinc finger, C2H2-like
SuperFamilySSF576672.47E-615031539No hitNo description
PROSITE profilePS5015712.94415031532IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.7E-615041531IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028015051527IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.2E-815321557IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001415331557IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.74115331562IPR007087Zinc finger, C2H2
PROSITE patternPS00028015351557IPR007087Zinc finger, C2H2
SuperFamilySSF576674.52E-915431587No hitNo description
Gene3DG3DSA:3.30.160.607.9E-915581586IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.46815631594IPR007087Zinc finger, C2H2
SMARTSM003550.9615631589IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028015651589IPR007087Zinc 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: 1597 aa     Download sequence    Send to blast
MRATEKKSGI MGGGSEGNAD VLPWLKSMPV APVYRPTAEE FQDPIGYIFK IEKEASKYGI  60
CKIIPPFPPS PKKTAIANLN RSLAVSGSTF TTRQQQIGFC PRRPRPVQRP VWQSGDHYTF  120
TEFESKAKSF EKAYLKRHTR KGSGSGPGPG PTPLETETLF WKATLDKPFS VEYANDMPGS  180
AFSPKCRHAG DPTSLADTPW NMRAVSRATG SLLRFMKEEI PGVTSPMVYV AMLFSWFAWH  240
VEDHDLHSLN YLHMGAGKTW YGVPRDAAVA FEEVVRVHGY GGEINPLVTF AILGEKTTVM  300
SPEVFISAGV PCCRLVQNAG EFVVTFPRAY HTGFSHGFNC GEAANIATPE WLRVAKDAAI  360
RRASLNYPPM VSHFQLLYDL ALALCSRIPA SVSAGPRSSR LKDKKKGEGE TVIKELFVQD  420
VLQNNDLLHI LGKGSAVVLL PRSSVDISVC SKLRVGSQQS INVSNSEGMH SSKGFVSDDL  480
VFNRSHGIKQ EKSFYSVKDK FTTMYERNRI SSFDVNGNSS TSSSKPLQRD TEGETSEEDG  540
LSDQRLFSCV TCGILSFSCV AIVQPRDPAA RYLMSADCSF FNDWVVGSGV SNSKFTTAPE  600
EATIPVSNMY TGWMKKNVQD GMQDVSVQSS RDALNIESEK GNSALALLAS AYGNSSDSEE  660
DQISADGHET NVLNSASESL LSHTQDSHAS PMPALDSADN IPSKSASCED LMHHRFECNL  720
SHQSLDHSLK KQEYNITSGV TFENMRTVPN STSNCSQDAH DAERSLSKMS MVPFDNKNSS  780
MVLQSDEDSS RMHVFCLEHA AEAEKQLRPI GGAHIFLLCH PDYPKIEAEA KVVAEDLGID  840
YTWKSIAYRH ASKDDGERIQ SALDSEEAIP GNGDWAVKLG INLFYSAYLS RSPLYSKQMP  900
YNSVIYCAFG CSSPSSLPEE PKVYQRRVNR QKKVVAGKWC GKVWMSNQVH PLLAKRDSED  960
AEDEKMLLGW ILPDARIERS ESTPKSETTS RKSGKKRKMT AENGRTRKGS YAKKNVVSYN  1020
STEDKPNSQP RRIHRSKKAR NVERDRAALK GDSSPYHHRK PISKQTNCTE SDAVSDDSVD  1080
DEDDHMQHGR NFDIDNDVVS NDTGDCDSDW QQREEHSSKD VEDMERDAIS EDSLDVGSLQ  1140
LQRKTSEGKH AKCTSEEDII SDDQMESCFQ KRQRRTPKSR QAKYLSGKNI TSDDQLELKM  1200
QKEQRRNPKN RQDKYLNEED IDSDDQLEGH YRRYQRRNPK GRQAKCVAEE DEMSGDQLED  1260
HCQKLQTSFS RKKQIKGIDR EVKYVMSDDQ LEDHFPKQQR RTPKSRQNKY TDKEVMDDSA  1320
ENNSRVLHRT PKRKQDKSMD EDDLNSDDEM EDDQQLRRTL RSKQSKPKTL QQMKQANSLQ  1380
AKSQASRSIK RGSRVLVKSK IPQQIKPRNK QSSNSREFSL LMEDEEEGGP STRLRKRTTK  1440
AQESEGKLKD KQTKRKKVKN ATTAKVSVGH AKGKDGDADY QCDIDGCSMS FGSKQELLHH  1500
KRNICPVKGC GKKFFSHKYL VQHRRVHEDE RPLKCPWKGC KMTFKWAWAR TEHIRVHTGA  1560
RPYVCAEQGC GQTFRFVSDF SRHKRKTGHS AKKSRQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A2e-80203844353Transcription factor jumonji (Jmj) family protein
6ip4_A2e-80203844353Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
114341456RKRTTKAQESEGKLKDKQTKRKK
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
PlantRegMapPhvul.009G169700.1
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_007137965.10.0hypothetical protein PHAVU_009G169700g
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLV7AWK50.0V7AWK5_PHAVU; 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]