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 Thecc1EG008716t2
Common NameTCM_008716
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: 200aa    MW: 22921.2 Da    PI: 6.1555
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG008716t2genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF89.61.6e-28959151
                      S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
            SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                      krie+ks rqvtfskRr g++KKA ELSvLCd+e+a++ifss+g+lye+ss
  Thecc1EG008716t2  9 KRIEDKSSRQVTFSKRRSGLIKKARELSVLCDVEIALVIFSSRGRLYEFSS 59
                      79***********************************************96 PP
2K-box46.31.8e-16761621298
             K-box  12 akaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                       +++e ++   + L++ +e L   q +l   ++e+Lsl +L +Le+qL+ +l++ R++K++l++e+i +lq+kek l+ en+ L+++ 
  Thecc1EG008716t2  76 QESEASKDVNEALRSHTELLHIVQSQLEEPNVEQLSLMDLVNLEKQLDMALSETRARKTQLMMESIMTLQEKEKLLRAENELLERES 162
                       4555555556678999999999999999999****************************************************9876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006631.721161IPR002100Transcription factor, MADS-box
SMARTSM004321.3E-37160IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.83E-30277IPR002100Transcription factor, MADS-box
CDDcd002658.25E-38271No hitNo description
PRINTSPR004041.7E-28323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003194.5E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004041.7E-282338IPR002100Transcription factor, MADS-box
PRINTSPR004041.7E-283859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129711.8178168IPR002487Transcription factor, K-box
PfamPF014861.1E-1281161IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009910Biological Processnegative regulation of flower development
GO:0010048Biological Processvernalization response
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: 200 aa     Download sequence    Send to blast
MGRRKVQMKR IEDKSSRQVT FSKRRSGLIK KARELSVLCD VEIALVIFSS RGRLYEFSSA  60
DGLTKILERY RCHYEQESEA SKDVNEALRS HTELLHIVQS QLEEPNVEQL SLMDLVNLEK  120
QLDMALSETR ARKTQLMMES IMTLQEKEKL LRAENELLER ESAAMEKNED EGNEVVIGFS  180
NHQYLGNLGS LCCPTPTRL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A6e-24188188MEF2C
5f28_B6e-24188188MEF2C
5f28_C6e-24188188MEF2C
5f28_D6e-24188188MEF2C
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the negative regulation of flowering time, probably through the photoperiodic and vernalization pathways; more efficient in cv. Landsberg erecta than in cv. Columbia background. Prevents premature flowering (PubMed:12724541, PubMed:25339407). Involved in the modulation of vernalization impact on flowering according to genotype acclimation to altitude (PubMed:25339407). {ECO:0000269|PubMed:12724541, ECO:0000269|PubMed:25339407}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Repressed during vernalization (PubMed:12724541). Regulated by HAM1 and HAM2 via epigenetic modification of chromatins at H4K5 acetylation during flowering (PubMed:23273925). {ECO:0000269|PubMed:12724541, ECO:0000269|PubMed:23273925}.
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_007043954.21e-132PREDICTED: agamous-like MADS-box protein AGL27 isoform X1
SwissprotQ9LSR72e-53AGL70_ARATH; Agamous-like MADS-box protein AGL70
TrEMBLA0A061E6191e-142A0A061E619_THECC; Flowering locus C, putative isoform 2
STRINGEOX997861e-143(Theobroma cacao)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM9861987
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G65060.12e-50MIKC_MADS family protein
Publications ? help Back to Top
  1. Conte MG,Gaillard S,Droc G,Perin C
    Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants.
    BMC Genomics, 2008. 9: p. 183
    [PMID:18426584]
  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]
  4. Nasim Z,Fahim M,Ahn JH
    Possible Role of MADS AFFECTING FLOWERING 3 and B-BOX DOMAIN PROTEIN 19 in Flowering Time Regulation of Arabidopsis Mutants with Defects in Nonsense-Mediated mRNA Decay.
    Front Plant Sci, 2017. 8: p. 191
    [PMID:28261246]