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 Aradu.HLK79
Organism
Arachis duranensis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Dalbergieae; Arachis
Family C2H2
Protein Properties Length: 1577aa    MW: 178094 Da    PI: 8.3035
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Aradu.HLK79genomeNCGR_PGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.10.000614621487123
                   EEET..TTTEEESSHHHHHHHHHH.T CS
      zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                   ++C    C++sF +k +L++H r+ +
  Aradu.HLK79 1462 FQCDidGCTMSFGSKQELMHHKRNiC 1487
                   89********************9877 PP
2zf-C2H212.70.0003814871509323
                   ET..TTTEEESSHHHHHHHHHHT CS
      zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                   Cp   Cgk F ++ +L++H r+H
  Aradu.HLK79 1487 CPvkGCGKKFFSHKYLVQHRRVH 1509
                   9999*****************99 PP
3zf-C2H211.70.0007715451571123
                   EEET..TTTEEESSHHHHHHHHHH..T CS
      zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                   y+C    Cg++F+  s++ rH r+  H
  Aradu.HLK79 1545 YVCAepGCGQTFRFVSDFSRHKRKtgH 1571
                   899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.1E-151758IPR003349JmjN domain
PROSITE profilePS5118314.3541859IPR003349JmjN domain
PfamPF023753.4E-141952IPR003349JmjN domain
SuperFamilySSF511977.14E-26103134No hitNo description
SuperFamilySSF511977.14E-26189358No hitNo description
SMARTSM005588.3E-52192361IPR003347JmjC domain
PROSITE profilePS5118433.411192361IPR003347JmjC domain
PfamPF023737.6E-36225344IPR003347JmjC domain
Gene3DG3DSA:3.30.160.605.3E-414541484IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003559.114621484IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.50814851514IPR007087Zinc finger, C2H2
SMARTSM003550.004514851509IPR015880Zinc finger, C2H2-like
SuperFamilySSF576676.66E-614851521No hitNo description
Gene3DG3DSA:3.30.160.601.2E-514871513IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028014871509IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.603.7E-815141539IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001415151539IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.74115151544IPR007087Zinc finger, C2H2
PROSITE patternPS00028015171539IPR007087Zinc finger, C2H2
SuperFamilySSF576672.89E-915251569No hitNo description
Gene3DG3DSA:3.30.160.602.4E-915401568IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.26115451576IPR007087Zinc finger, C2H2
SMARTSM003550.6215451571IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028015471571IPR007087Zinc 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: 1577 aa     Download sequence    Send to blast
MAEANGDVFQ WLKSMPLAPE YRPTLTEFQD PIAYIFKIEK EASKYGICKI IPPFPPPPRK  60
VAIANFTRSL TKPDEPNSKP TFTTRQQQIG FCPRRPRPVQ RPVWQSGENY TFQEFEAKAK  120
AFEKSYLKKH HLHHQGHRKG GGGGGGSGGL GPLEVETLFW KATVDKPFSV EYANDMPGSA  180
FSRKCREECA AALAESAWNM REISRANGSL LRFMKEEIPG VTSPMVYLAM LFSWFAWHVE  240
DHDLHSLNYL HMGSGKTWYG VPRDAAVAFE DVVRVHGYGS EINPLVTFST LGEKNTVMSP  300
EVLINAGVPC CRLVQNAGEF VVTFPRAYHT GFSHGFNCGE AANIATPEWL RVAKDAAIRR  360
ASVNHSPMVS HFQLLYDLAL ALCSRFVFCY YGFLLLAVTG IPELFVQDVS QNNDLLQELS  420
KGSEIILLPR SSFDISLCSK LRSGSKQRKV NSRFSLGACN SEEMNSSKGF VSDDLAFSMN  480
RGIKQEGSLS IKDKITSLCE RSMISSYDVN GNICSSSSKQ LQGDNERESG EGDGSPDKRL  540
FSCVTCGILC FPCVAIVQPR ESAARYLMSA DCSFFNDWVV GSGVSSKKFI AHEEAAFPEP  600
RWTEKKTQGL YQDPVQSAQY QLQTAERNYE ESLGKSNTAL ALLASTYGNS SDSEEEHGDS  660
DIVVDGHESP MINATLGGSP SNFQDGCTIP LTGPDSRNDF SHQSFDHSLE KQDCDTSSGF  720
ALKNMRAMYT NDTEKTLLGK AMVPNDDKNA SVMPQGDQDS SRMHVFCLEH AVEAEQQLRP  780
IGGAHIMLLC HPDFPKIEAE AKLVAEDLGI DYLWKKIEYR HSSKEDEERI QVALDSEEAI  840
PGNGDWCVKL GINLFYSSTL SRSPLYSKQM PYNSVIYYAF GQSSPASSPL EPKVYQRRVN  900
KQKKIVAGKW CGKVWMSSQV HPLLAKRDSE DVEDEKSLHG WGLHDEKIER SGSIPKSETS  960
ARKSGKKRKM TIENGRARKG SFAERDVDLD NPTEDKPNQQ LRRTLRSKQA RDIESEGADL  1020
EGDYSPPYHR KPLSDQTNCT GSDAVSDDSL DDKFIDNDVV SDDTMVYDSD CHQRFEHSSM  1080
QVEDIEDAVS EDSLDDGSLQ LHRKNSKSKH ARYIRKGRCI AEKEEMMSDD QLEPHKKNKQ  1140
QRNPKSRQAK YLAREDAISH GQLEGHCRKY RKTPKGRLAK YVAGEDVSSD EQLENYSRKQ  1200
QTSLPKRQKN KGVLTDDQLE DHFQKQQKSV SRRRQNKGIE RGVKDEMSDD QLEDHVQKQQ  1260
TSVSKRRRNK QIERDDVMSD DEMEDHFQKQ RSSIPRNRQN SNSHLAHKTP KRKQAKCVDD  1320
DDGDDDDVNS DDEVEDDSQQ KQQRTLRSKQ SKPMTLKQMK QARSLQMKNQ TSRSVKRGAQ  1380
TLKKLKASQI RNKQSGKSRE FSLKMEEGEE GGPSTRLRKR APKVEESDGI SKEKQTKKKR  1440
VKNATSAKAA SNAKVKDEEN EFQCDIDGCT MSFGSKQELM HHKRNICPVK GCGKKFFSHK  1500
YLVQHRRVHE DDRPLKCPWK GCKMTFKWAW ARTEHIRVHT GARPYVCAEP GCGQTFRFVS  1560
DFSRHKRKTG HSTKKSR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A4e-7573824353Transcription factor jumonji (Jmj) family protein
6ip4_A4e-7573824353Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
114171439RKRAPKVEESDGISKEKQTKKKR
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
PlantRegMapAradu.HLK79
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025688566.10.0lysine-specific demethylase REF6 isoform X2
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A445AAM70.0A0A445AAM7_ARAHY; 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]