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 KHN31931.1
Organism
Glycine soja
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; Glycine; Soja
Family C2H2
Protein Properties Length: 1244aa    MW: 142418 Da    PI: 9.1896
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
KHN31931.1genomeTCUHKView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.30.0005311281153123
                  EEET..TTTEEESSHHHHHHHHHH.T CS
     zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                  y+C    C++sF +k +L++H ++ +
  KHN31931.1 1128 YQCDidGCTMSFGSKQELMHHKKNiC 1153
                  99*******************99866 PP
2zf-C2H213.20.0002611531175323
                  ET..TTTEEESSHHHHHHHHHHT CS
     zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                  Cp   Cgk F ++ +L++H r+H
  KHN31931.1 1153 CPvkGCGKKFFSHKYLVQHRRVH 1175
                  9999*****************99 PP
3zf-C2H213.80.0001712111237123
                  EEET..TTTEEESSHHHHHHHHHH..T CS
     zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                  y+C   dCg++F+  s++ rH r+  H
  KHN31931.1 1211 YVCAepDCGQTFRFVSDFSRHKRKtgH 1237
                  899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005452.0E-152061IPR003349JmjN domain
PROSITE profilePS5118313.8132162IPR003349JmjN domain
PfamPF023751.0E-132255IPR003349JmjN domain
SuperFamilySSF511974.67E-11176267No hitNo description
SMARTSM005583.7E-9180405IPR003347JmjC domain
PROSITE profilePS5118416.301180326IPR003347JmjC domain
PfamPF023739.3E-15213265IPR003347JmjC domain
Gene3DG3DSA:3.30.160.608.8E-411201150IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.08E-511241180No hitNo description
SMARTSM003558.111281150IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.94411511180IPR007087Zinc finger, C2H2
SMARTSM003550.004511511175IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.4E-611521179IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028011531175IPR007087Zinc finger, C2H2
SuperFamilySSF576673.08E-911671209No hitNo description
Gene3DG3DSA:3.30.160.609.2E-911801205IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001411811205IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.74111811210IPR007087Zinc finger, C2H2
PROSITE patternPS00028011831205IPR007087Zinc finger, C2H2
SuperFamilySSF576675.67E-811991233No hitNo description
Gene3DG3DSA:3.30.160.606.6E-912061234IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.69712111242IPR007087Zinc finger, C2H2
SMARTSM003551.112111237IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012131237IPR007087Zinc 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:0032259Biological Processmethylation
GO:0033169Biological Processhistone H3-K9 demethylation
GO:0035067Biological Processnegative regulation of histone acetylation
GO:0048366Biological Processleaf development
GO:0055114Biological Processoxidation-reduction process
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0008168Molecular Functionmethyltransferase activity
GO:0016491Molecular Functionoxidoreductase activity
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 1244 aa     Download sequence    Send to blast
MGVVSEGNGD VLPWLKSMPV APEYRPSAAE FQDPISYIFK IEKEASKYGI CKIIPPFPPS  60
SRKTAIANLN RSLVETGSTF TTRQQQIGFC PRRPRPVQRP VWQSGDRYTF TEFESKAKSF  120
EKTYLKRHAK KASGLGPGPL ETETLFWKAT LDKPFSVEYA NDMPGSAFSP KCRRVGDPSS  180
LADTQWNMRA VSRAKGSLLQ FMKEEIPGVT SPMVYVAMLF SWFAWHVEDH DLHSLNYLHM  240
GAGKTWYGVP RDAAVAFEEV VRVHGYGGEI NPLGWMKKNV QDGIHDVPFQ SSQVALNTVS  300
ENGNTALALL ASAYGNSSDS EEDQIAVDSH ESNVINSASE SLLSDTRDSH ASRTALDRGD  360
YIPSKSSSYE DFIHRRLECF ENTRTVPNST SNCSQDAYDA KRSLSSKSMV PFDYKKALMV  420
LQSDEDSSRM HVFCLEHAAE AEQQLRSIGG ADILLLCHPD YPKIEAEAKM VAEDLGIDYV  480
LKNIVYRHAS TEDEERIQSA LDNEEAIPGN GDWAVKLGIN LFYSANLSRS PLYSKQMPYN  540
SVIYSAFGCS SPASSLVEPK VYQRRVNKQK KIVAGKWCGK VWMSNQVHPL LAKRDSEDIE  600
DEKLLQGLTL PDEKIERSES TLKREAISRK SGKKRKKTAE NGRFRKGSYA KKNILSDDST  660
EDKPNSQPRR ILRSKKARHV ERDCAALKRD YSPPYHHRKP TSHQTNFTES DAVSDDSLDD  720
DDHMRQRRNV KVEKAKFMDN DVVSNDTMDY DSDCQQREEH SSKQVEDMER DANSEDFLDV  780
GSLQLQRKIS RAMHVKSIRE EDIISDDQME SPFQKRQKRI PKSRQGKYLT GKDIISDDQL  840
ELKMQKRQQT NPKSRQAKYL NKEDIASDDQ LENHCQKQQT NFSRKRQNKD VVREVKNEMC  900
DDQLENHCQK QQTNFSRKRQ NKDVVREVKN EMCDDQLEDH FLKQHRRFPK SRQNKHTEKE  960
IMDDLAENNS HLLHRTPKRK QAKCMEEDDM NSDDEMEDDQ PLRRALRSKQ AKPKTLLKQA  1020
NSFQAKKQAS RPIKQGSRLL VKSKAPQQIK QPAHLRNKQS NNTQEFSLYM EEEEDGGPST  1080
RLRKRATKAQ ESEGKLKDKQ TKRKKVKNAA AAKVSVGDAR MQDGEAEYQC DIDGCTMSFG  1140
SKQELMHHKK NICPVKGCGK KFFSHKYLVQ HRRVHEDERP LKCPWKGCKM TFKWAWARTE  1200
HIRVHTGARP YVCAEPDCGQ TFRFVSDFSR HKRKTGHSAK KNCQ
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A1e-691126124221137Lysine-specific demethylase REF6
6a58_A1e-691126124221137Lysine-specific demethylase REF6
6a59_A1e-691126124221137Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1632636KKRKK
210821104RKRATKAQESEGKLKDKQTKRKK
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
PlantRegMapKHN31931.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2353400.0AC235340.1 Glycine max strain Williams 82 clone GM_WBb0086A04, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_028236971.10.0lysine-specific demethylase REF6-like
SwissprotQ9STM31e-120REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A0B2RBZ70.0A0A0B2RBZ7_GLYSO; Lysine-specific demethylase REF6
STRINGGLYMA06G18300.10.0(Glycine max)
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
AT3G48430.11e-113relative of early flowering 6
Publications ? help Back to Top
  1. Qi X, et al.
    Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing.
    Nat Commun, 2014. 5: p. 4340
    [PMID:25004933]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. Qiu Q, et al.
    DNA methylation repels targeting of Arabidopsis REF6.
    Nat Commun, 2019. 10(1): p. 2063
    [PMID:31048693]