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 Thecc1EG016147t1
Common NameTCM_016147
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 MIKC_MADS
Protein Properties Length: 216aa    MW: 24830.4 Da    PI: 9.6917
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG016147t1genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF96.98.7e-31959151
                      S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
            SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                      krien + rqvtfskRrng+lKKA+ELSvLCdaeva+iifs++gklye+ss
  Thecc1EG016147t1  9 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPRGKLYEFSS 59
                      79***********************************************96 PP
2K-box78.51.7e-2683172998
             K-box   9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                       + e+++ + ++++  + k+ie L+ ++R+llG++Le++s+++Lq Le+qLe+sl++iR++Kn+l+ eqie+l+  e++l een +Lr++ 
  Thecc1EG016147t1  83 ALEENMPNVKEDAHSMAKKIELLEDSKRKLLGNGLEPCSFNDLQLLESQLERSLSRIRARKNQLFWEQIEKLKGEERRLGEENAKLREQC 172
                       55788999*******************************************************************************985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006631.931161IPR002100Transcription factor, MADS-box
SMARTSM004321.5E-41160IPR002100Transcription factor, MADS-box
CDDcd002652.02E-44371No hitNo description
PRINTSPR004044.8E-31323IPR002100Transcription factor, MADS-box
SuperFamilySSF554553.14E-33372IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003195.1E-271057IPR002100Transcription factor, MADS-box
PRINTSPR004044.8E-312338IPR002100Transcription factor, MADS-box
PRINTSPR004044.8E-313859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129714.28388178IPR002487Transcription factor, K-box
PfamPF014867.1E-2689172IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010048Biological Processvernalization response
GO:0048510Biological Processregulation of timing of transition from vegetative to reproductive phase
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 216 aa     Download sequence    Send to blast
MVRGKTQMKR IENATSRQVT FSKRRNGLLK KAFELSVLCD AEVALIIFSP RGKLYEFSSS  60
SMNKTIERYQ KREKDYGICS KAALEENMPN VKEDAHSMAK KIELLEDSKR KLLGNGLEPC  120
SFNDLQLLES QLERSLSRIR ARKNQLFWEQ IEKLKGEERR LGEENAKLRE QCGMQPRQSP  180
TSQTDELHHV QSMEVETELF IGPPERRSAK NPSVN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A7e-20169169MEF2C
5f28_B7e-20169169MEF2C
5f28_C7e-20169169MEF2C
5f28_D7e-20169169MEF2C
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor that promotes flowering, especially in response to vernalization by short periods of cold, in an FLC-inpedendent manner. {ECO:0000269|PubMed:16778081}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Maintained at very low levels by the polycomb-group (PcG) proteins MSI1, CLF, and EMF2 via histone methylation (H3K27me3). Derepressed upon cold treatment (vernalization). {ECO:0000269|PubMed:16778081}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_007040082.11e-158PREDICTED: agamous-like MADS-box protein AGL19
SwissprotO827431e-78AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBLA0A061G5941e-156A0A061G594_THECC; AGAMOUS-like 14
STRINGEOY245831e-157(Theobroma cacao)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM7828413
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G22950.12e-71AGAMOUS-like 19
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. 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]
  3. Suter L,Rüegg M,Zemp N,Hennig L,Widmer A
    Gene regulatory variation mediates flowering responses to vernalization along an altitudinal gradient in Arabidopsis.
    Plant Physiol., 2014. 166(4): p. 1928-42
    [PMID:25339407]