PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Cc08_g13780
Common NameGSCOC_T00030304001
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Gentianales; Rubiaceae; Ixoroideae; Coffeeae; Coffea
Family MIKC_MADS
Protein Properties Length: 203aa    MW: 23476 Da    PI: 10.0154
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cc08_g13780genomeCGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF95.23e-30959151
                 S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
       SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                 krien + rqvtfskRr g+lKKA+ELSvLCdaeva+iifs++gklye+ss
  Cc08_g13780  9 KRIENATSRQVTFSKRRSGLLKKAFELSVLCDAEVALIIFSPKGKLYEFSS 59
                 79***********************************************96 PP

2K-box71.23.3e-248117110100
        K-box  10 eeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkklee 100
                    ++a++ ++e+a L+k+ie L+++ R++lG++L+s s+ eLqq+e+qLeksl+ iRs+K+ l++e +++l++ ek l++en +Lr k+ee
  Cc08_g13780  81 RMEQAQHFEEEVAILRKKIEILEETRRRFLGDGLDSSSVDELQQIENQLEKSLSIIRSRKSSLFRERMDQLKEEEKILRKENAELRGKYEE 171
                  56789*********************************************************************************99986 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004324.4E-41160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006632.001161IPR002100Transcription factor, MADS-box
CDDcd002657.45E-40275No hitNo description
SuperFamilySSF554558.89E-33387IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004041.3E-30323IPR002100Transcription factor, MADS-box
PfamPF003198.4E-271057IPR002100Transcription factor, MADS-box
PRINTSPR004041.3E-302338IPR002100Transcription factor, MADS-box
PRINTSPR004041.3E-303859IPR002100Transcription factor, MADS-box
PfamPF014867.3E-2483169IPR002487Transcription factor, K-box
PROSITE profilePS5129714.60385175IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
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: 203 aa     Download sequence    Send to blast
MARGKTQMKR IENATSRQVT FSKRRSGLLK KAFELSVLCD AEVALIIFSP KGKLYEFSSS  60
SATSTIERYQ KNIKNLCPSR RMEQAQHFEE EVAILRKKIE ILEETRRRFL GDGLDSSSVD  120
ELQQIENQLE KSLSIIRSRK SSLFRERMDQ LKEEEKILRK ENAELRGKYE EQQLELSISP  180
QPLPLRQVKE VETQLFIGPP KS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A8e-19169169MEF2C
5f28_B8e-19169169MEF2C
5f28_C8e-19169169MEF2C
5f28_D8e-19169169MEF2C
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKJ4832260.0KJ483226.1 Coffea arabica TM3-1 (TM3-1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_027082904.11e-141agamous-like MADS-box protein AGL19
RefseqXP_027083082.11e-141agamous-like MADS-box protein AGL19
SwissprotO827438e-70AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBLA0A068UN111e-141A0A068UN11_COFCA; Uncharacterized protein
STRINGXP_009772098.11e-83(Nicotiana sylvestris)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA4024625
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G22950.11e-65AGAMOUS-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. 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]