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 Thecc1EG014549t2
Common NameTCM_014549
Organism
Theobroma cacao
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma
Family C2H2
Protein Properties Length: 1648aa    MW: 186350 Da    PI: 8.602
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG014549t2genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.80.0003715581580323
                        ET..TTTEEESSHHHHHHHHHHT CS
           zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                        Cp   Cgk F ++ +L++H r+H
  Thecc1EG014549t2 1558 CPvkGCGKKFFSHKYLVQHRRVH 1580
                        9999*****************99 PP
2zf-C2H211.60.0008516161642123
                        EEET..TTTEEESSHHHHHHHHHH..T CS
           zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                        y+C    Cg++F+  s++ rH r+  H
  Thecc1EG014549t2 1616 YVCAeeGCGQTFRFVSDFSRHKRKtgH 1642
                        89********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.2E-152364IPR003349JmjN domain
PROSITE profilePS5118314.2432465IPR003349JmjN domain
PfamPF023753.8E-142558IPR003349JmjN domain
PROSITE profilePS5118433.26199368IPR003347JmjC domain
SMARTSM005582.2E-47199368IPR003347JmjC domain
SuperFamilySSF511976.04E-26213385No hitNo description
PfamPF023735.2E-35232351IPR003347JmjC domain
SMARTSM003552615331555IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.36215561585IPR007087Zinc finger, C2H2
SMARTSM003550.004515561580IPR015880Zinc finger, C2H2-like
SuperFamilySSF576674.41E-615561592No hitNo description
Gene3DG3DSA:3.30.160.602.3E-515571584IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028015581580IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.603.9E-815851610IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001415861610IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.74115861615IPR007087Zinc finger, C2H2
PROSITE patternPS00028015881610IPR007087Zinc finger, C2H2
SuperFamilySSF576673.23E-915961640No hitNo description
Gene3DG3DSA:3.30.160.603.3E-916111639IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.8516161642IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.2416161647IPR007087Zinc finger, C2H2
PROSITE patternPS00028016181642IPR007087Zinc 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: 1648 aa     Download sequence    Send to blast
MAASSLSPEP SQEVFSWLKS LPLAPEYRPT LAEFQDPIAY IFKIEKEASQ YGICKIIPPV  60
PPAPKKTAIG NLNRSLLARA AANTSSDSKP APTFTTRQQQ IGFCPRKPRP VQKPVWQSGE  120
YYTFQEFEAK AKNFERGYLK RYSRKGSLSA LEVETLFWKA TVDKPFSVEY ANDMPGSAFV  180
PLSSKKSSGG GREAGEGVTV GETPWNMRAV SRAKGSLLRF MKDEIPGVTS PMVYIAMLFS  240
WFAWHVEDHD LHSLNYLHMG AGKTWYGVPR DAAVAFEEVV RLDGYGGEFN PLVTFSTLGE  300
KTTVMSPEVF VHAGIPCCRL VQNAGEFVVT FPRAYHSGFS HGFNFGEAAN IATPEWLRVA  360
RDAAIRRASI NYPPMVSHFQ LLYDLALELC SRVPMSINAK PKSSRLKDKK KSEGETLVKE  420
LFVQNLMQNN ELLHILGKGS SVVLLPKSSS DISPCSDLRV ASQIRINPRM SRGLCNYKDV  480
VKLSKDLASD EIMVGGNEEI KGVKGFYSVK GKFASMYEGN RDSAFNGTDH LCRLPLQTLN  540
MSAEGENAVQ GDALSDQGLF SCVTCGILCF SCIAVLQPTE QAARYLMSAD CSFFNDWTVG  600
SGVTRDGFTT THGDVITSEQ NSCTRWMNKR APNALYDVPV QSVEDKFHMA DQSNQVVEDT  660
EKGGDTSALG LLASTYGNSS DSEEDHVEPN VTVSGDETNS ANRSLERKFQ YNGSGFSPGD  720
ANGSNNPSLL RLESEEEAPV HVDIKSTSPQ AFDHTVEFET DNLASRRSIG LEDKFRDPIT  780
TSHANPSYSP ATHGAEKMRF SKTMVPMENA DIPFAPRSDE DSSRMHVFCL EHAVEVDQQL  840
RQIGGVHVFL LCHPEYPKIE AEAKLVTEEL GIDYPWNDIL FGDATKEDEE RIQSALDSED  900
AIPGNGDWAV KLGVNLFYSA NLSRSTLYSK QMPYNYVIYS AFGRNSPGSS PTKLNVYGRR  960
SGKQKKVVAG KWCGKVWMSN QVHPFLAQRD PEEQEQERGF HAWATSDENL ERKPENVHKA  1020
ETTKVAKKFN RKRKMRPEIA SSKKVKCIET EGAVSDDSLD GGSLRQQQIF FRGKQPRLIQ  1080
KEEAISYDLL EDDSLLQQRN LSRKKLAKFI EREGAESEDA EEEFTHQQHW RNLRGKQGKY  1140
IEEDDAVSGD SLDESSLKQY RRIPRSWQAK FREREDIVSE DELEEISHRL HRRIPRCRQI  1200
KSCEKNDAIS DDSRADNSLK QYRRMPKGRQ ANFVERDDTM SDDASEDDSQ HQLRRIPKGK  1260
QMKCMERDDA FSDDSLEDNL QQQHRIPRSK VAKFTDREDV VSFDSLKGSS HQQRRRVSRS  1320
QLTKFIERED AVSSDSPDDS SLQQLRRIPR SKQTKILERE DAVSDDSLDD TSQQQLRKTP  1380
RSRQGKFIER EDAVSYDSLD ENYHQPNRRT LRSRKKKAQT PRQIKQETPR NVKQGKRRTT  1440
KQVVSQQIKQ ETPRNRNTKI EQSARQCNSY GEDELEGGPS TRLRKRVRKP LKESETKPKE  1500
KKQASKKKVK NASNVKTLAG HNTSKVRDEE AEYQCDMEGC TMSFGLKQEL LLHKRNICPV  1560
KGCGKKFFSH KYLVQHRRVH LDDRPLKCPW KGCKMTFKWA WARTEHIRVH TGARPYVCAE  1620
EGCGQTFRFV SDFSRHKRKT GHSAKKG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A5e-75174248381Transcription factor jumonji (Jmj) family protein
6ip4_A5e-75174248381Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
114811487RLRKRVR
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
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_007037855.20.0PREDICTED: lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A061FYM00.0A0A061FYM0_THECC; Relative of early flowering 6, putative isoform 1
TrEMBLA0A061FZP00.0A0A061FZP0_THECC; Relative of early flowering 6, putative isoform 2
STRINGEOY223560.0(Theobroma cacao)
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. Motamayor JC, et al.
    The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color.
    Genome Biol., 2013. 14(6): p. r53
    [PMID:23731509]
  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]