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 KHN05795.1
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: 765aa    MW: 88706.5 Da    PI: 9.8933
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
KHN05795.1genomeTCUHKView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.80.00017649674123
                 EEET..TTTEEESSHHHHHHHHHH.T CS
     zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                 y+C    C++sF +k +L++H r+ +
  KHN05795.1 649 YQCDidGCTMSFGSKQELMHHKRNiC 674
                 99********************9877 PP
2zf-C2H213.90.00016674696323
                 ET..TTTEEESSHHHHHHHHHHT CS
     zf-C2H2   3 Cp..dCgksFsrksnLkrHirtH 23 
                 Cp   Cgk F ++ +L++H r+H
  KHN05795.1 674 CPvkGCGKKFFSHKYLVQHRRVH 696
                 9999*****************99 PP
3zf-C2H214.50.0001732758123
                 EEET..TTTEEESSHHHHHHHHHH..T CS
     zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt..H 23 
                 y+C   dCg++F+  s++ rH r+  H
  KHN05795.1 732 YVCAepDCGQTFRFVSDFSRHKRKtgH 758
                 899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.601.2E-4638671IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.23E-5645701No hitNo description
SMARTSM003557.3649671IPR015880Zinc finger, C2H2-like
SMARTSM003550.0045672696IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.944672701IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.607.6E-7673700IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS000280674696IPR007087Zinc finger, C2H2
SuperFamilySSF576671.7E-9688730No hitNo description
Gene3DG3DSA:3.30.160.605.2E-9701726IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.0014702726IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.741702731IPR007087Zinc finger, C2H2
PROSITE patternPS000280704726IPR007087Zinc finger, C2H2
SuperFamilySSF576672.79E-8720754No hitNo description
Gene3DG3DSA:3.30.160.603.3E-9727755IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.697732763IPR007087Zinc finger, C2H2
SMARTSM003551.1732758IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280734758IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0032259Biological Processmethylation
GO:0003676Molecular Functionnucleic acid binding
GO:0008168Molecular Functionmethyltransferase activity
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 765 aa     Download sequence    Send to blast
MWKNIEYSHA SKEDEEKIQS ALDSEEAIPG NGDWAVKLGI NLFYSANLSR SPLYSKQMPY  60
NSVIYSAFGC SSPASSPVEP KVYQRRVNRQ KKIVAGKWCG KVWMSNQVHP LLAKRDFEDI  120
EDEKLLIGLI LPDDKIERSE STPKSEATSR KSGKKRKKTA ENGRFRKGSY ANKNLLSDNS  180
TEDKPNLLPR SILRSKKVRH VERDCAALKG GYSPPYHHRK PSNNQTNFTE SYAVSDDSLD  240
DDDHMQQRRN VKIEKAKFMD NDVVSNDTMD NDSDWQQRED VSSKQVEDTE GDAISEDSLD  300
VGSLQLQRKT SKGKHPKYIG EEDIISDDQM ESHFQKRQKR IPESRQGKYL TGKDIISDDQ  360
LELKMKKQQR RNPKSRQAKY LNEEDIASDD QLEGHYRRYQ RKNPKGRQAT CVAGEDQMSD  420
DQLENHCQKQ QTSFYRKRQN KGIEREVKNE MSDDHLEDHF LKQQQRFPKS RRNKHTDKED  480
TDDLAENNSH LLRRTPKRKQ AKCMEDDDMN SDDEMEDDQQ LRRTLRSKQA KPKTLQQMKQ  540
ANSLQAKKQA SRPIKQCSRM LVKSKAPQQI KQPSHLPNKQ SNNTQEFSLD MEEEEEGGPS  600
TRLRKRATKA QESERKLKHK QTKRKKVKNA AAAKVSVGHA KMKDGEAEYQ CDIDGCTMSF  660
GSKQELMHHK RNICPVKGCG KKFFSHKYLV QHRRVHEDER PLKCPWKGCK MTFKWAWART  720
EHIRVHTGAR PYVCAEPDCG QTFRFVSDFS RHKRKTGHSA KKNCQ
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A3e-7264776321137Lysine-specific demethylase REF6
6a58_A3e-7264776321137Lysine-specific demethylase REF6
6a59_A3e-7264776321137Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1153157KKRKK
2492498RRTPKRK
3492499RRTPKRKQ
4603625RKRATKAQESERKLKHKQTKRKK
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
PlantRegMapKHN05795.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
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_028229374.10.0lysine-specific demethylase JMJ705-like
SwissprotQ9STM34e-71REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A0B2P8Y40.0A0A0B2P8Y4_GLYSO; Lysine-specific demethylase REF6
STRINGGLYMA04G36630.10.0(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
AT5G04240.11e-45C2H2 family protein
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]