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 evm.model.supercontig_4.49
Organism
Carica papaya
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Caricaceae; Carica
Family C2H2
Protein Properties Length: 1536aa    MW: 172410 Da    PI: 8.9825
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
evm.model.supercontig_4.49genomeASGPBView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2130.0003114441466323
                                  ET..TTTEEESSHHHHHHHHHHT CS
                     zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                                  Cp   Cgk F ++ +L++H r+H
  evm.model.supercontig_4.49 1444 CPvkGCGKKFFSHKYLVQHRRVH 1466
                                  9999*****************99 PP
2zf-C2H211.80.0007515021528123
                                  EEET..TTTEEESSHHHHHHHHHH..T CS
                     zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                                  y+C    Cg++F+  s++ rH r+  H
  evm.model.supercontig_4.49 1502 YVCAeaGCGQTFRFVSDFSRHKRKtgH 1528
                                  89********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005452.9E-162364IPR003349JmjN domain
PROSITE profilePS5118314.8532465IPR003349JmjN domain
PfamPF023752.1E-142558IPR003349JmjN domain
SMARTSM005581.2E-49200369IPR003347JmjC domain
PROSITE profilePS5118433.752203369IPR003347JmjC domain
SuperFamilySSF511974.94E-26216383No hitNo description
PfamPF023731.4E-36233352IPR003347JmjC domain
SMARTSM003552314191441IPR015880Zinc finger, C2H2-like
SMARTSM003550.004514421466IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.44514421471IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.4E-514441465IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028014441466IPR007087Zinc finger, C2H2
SuperFamilySSF576671.79E-914581500No hitNo description
Gene3DG3DSA:3.30.160.601.7E-914661494IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001414721496IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.74114721501IPR007087Zinc finger, C2H2
PROSITE patternPS00028014741496IPR007087Zinc finger, C2H2
SuperFamilySSF576671.26E-714901524No hitNo description
Gene3DG3DSA:3.30.160.601.1E-814951525IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.9115021528IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.44815021533IPR007087Zinc finger, C2H2
PROSITE patternPS00028015041528IPR007087Zinc 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: 1536 aa     Download sequence    Send to blast
MAASTLSSDP TQEVFPWLKS LPLAPEFHPT FAEFQDPIAY IFKIEKEASK YGICKIVPPV  60
PPAPKKSAIT NLNRSLAARA ASAGAATSKP LPTFTTRQQQ IGFCPRKPRP VQKPVWQSGE  120
YYSFPEFEAK AKSFEKTYLK KCGKKGSLSP LEVETLYWKA TVDKPFSVEY ANDMPGSAFV  180
PVTGKKSVGV GGREAGEGVT VGETAWNMRG VSRAEGSLLR FMKEEIPGVT SPMVYIAMMF  240
SWFAWHVEDH DLHSLNYLHM GAGKTWYGVP RDAAVAFEEV VRVHGYGGEV NPLVTFATLG  300
EKTTVMSPEV FVSAGVPCCR LVQNAGEFVV TFPRAYHSGF SHGFNCGEAA NIATPEWLRV  360
AKDAAIRRAS INYPPMVSHF QLLYDLALAL CSRIPMNVSA KPRSSRLKDK KKGEGETLVK  420
ELFVQNVIQN NDLLHFLGKG SSAILLPEGS SDISVCSDLR VGSQLRAHPR MPLGACSYSD  480
VIKSSKGLDS GNDVLGSSDG MKPVKGTLAS QSLSKDTERE SSVQGDGLSD QRLFSCVTCG  540
ILSFACVAVV QPREAAARYL MSADCSFFND WTVSSGVTSE GFTLASRDTI ISEPRSRTRW  600
TEKSSQDGLF DVPVQSVDYQ IEMVNQANEG VSDTQMRGET SALGLLASTY GDSSDSDEDH  660
HATEARSPLL LRENSGDETS LRNIDCYEEP GYTRSNFKSR SDQTFDNSEF ETDNLTSPRS  720
NSLDSASKEL VMASNATSNC SPVSFVAEKT RFSRMIMPVE KADMPYAQKS DEDSSRLHVF  780
CLEHAVEVEK QLRPIGGVHI MLLCHPEYPR IEAEAKLVAE ELGIDYLWND IKFQVATRED  840
KERIQSALDS EEAIPGNGDW AVKLGINLFY SAVLSRSPMY TKQMPYNSVI YSAFGRSSPA  900
SSPSKSNSHG RRPAKQRKVV VGKWCGKVWM SNQVHPFLAQ RDLEEQEQER SFHARAIADE  960
NLENKPENIH KAQTTLETRK YSRKRKTATE IVPMKKIKPI ETEPVIPEGS LEDGSYKQHR  1020
RVSRSKQTKY VEKEDAVSCD SLEQNTRQWH RRSSRRKLAK TVEREDSLSD DPLEDNSLLK  1080
QRRILRGKRV EHFESDDAIS IGSLGDNSPL QQRRTLGSKQ TTFIEREDAG SDDDLVDDSH  1140
HHYQRISRGK ETQYVERDFT LSDDSMEDDS LQLDRRGLGN RQTTLTEMEG VVSCDSSEDH  1200
SQQQRSRTRR SKETKFVNKE DAGSYDSLED NSHQQPRKIP RGNQVKFIER EDTVSYDSLE  1260
DNCHPQGKRT QRSKKAKDIE REDGVSYDSL EDSSHQRRRR TLRSKKMKPK IIQKVKMETP  1320
QHMKKGKHLP AKQQTSRKKK QETPRQQNDK SGQNTRQFST YVEEQLEGGP STRLRKRILK  1380
SPKEIVVQVK EKKQTGKKKG KNASAGSSNA KVKDEEAEYL CDMEGCTMSF VSKQELVLHK  1440
RNICPVKGCG KKFFSHKYLV QHRRVHMDDR PLKCPWKGCK MTFKWAWART EHIRVHTGAR  1500
PYVCAEAGCG QTFRFVSDFS RHKRKTGHSA KKARG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A3e-73173908353Transcription factor jumonji (Jmj) family protein
6ip4_A3e-73173908353Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1981986SRKRKT
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
PlantRegMapevm.model.supercontig_4.49
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_021908879.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A061FYM00.0A0A061FYM0_THECC; Relative of early flowering 6, putative isoform 1
STRINGevm.model.supercontig_4.490.0(Carica papaya)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM52592843
Representative plantOGRP44011217
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]