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 Csa18g038770.1
Organism
Camelina sativa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Camelina
Family MIKC_MADS
Protein Properties Length: 199aa    MW: 22650.1 Da    PI: 9.398
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Csa18g038770.1genomeCSGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF75.54.1e-24959151
                    S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
          SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                    krie+k  rqvtf+kRrng++ KA  LSvLC+  va+ii+sstgkly +ss
  Csa18g038770.1  9 KRIEDKNSRQVTFCKRRNGLMEKARQLSVLCGSSVALIIVSSTGKLYSFSS 59
                    79***********************************************96 PP
2K-box34.87.1e-1311216745100
           K-box  45 sLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkklee 100
                     + s++ L ++e+qL+k+l+  R++K++l +e +++lq kek l+eenk L +++ e
  Csa18g038770.1 112 NVSIESLISIEEQLKKALSVTRARKTKLTMELVKTLQDKEKLLNEENKVLASQIRE 167
                     56899**********************************************99975 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006629.142161IPR002100Transcription factor, MADS-box
SMARTSM004324.0E-34160IPR002100Transcription factor, MADS-box
CDDcd002653.59E-33277No hitNo description
SuperFamilySSF554551.31E-27277IPR002100Transcription factor, MADS-box
PRINTSPR004044.8E-24323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003192.0E-231057IPR002100Transcription factor, MADS-box
PRINTSPR004044.8E-242338IPR002100Transcription factor, MADS-box
PRINTSPR004044.8E-243859IPR002100Transcription factor, MADS-box
PROSITE profilePS512979.76581171IPR002487Transcription factor, K-box
PfamPF014869.8E-9110165IPR002487Transcription 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: 199 aa     Download sequence    Send to blast
MGRRRVEIKR IEDKNSRQVT FCKRRNGLME KARQLSVLCG SSVALIIVSS TGKLYSFSSG  60
DSMAKILNHY YETQNVDDRR TVDLAEKTPD YLTNKELLEI VQCKLEEAKG DNVSIESLIS  120
IEEQLKKALS VTRARKTKLT MELVKTLQDK EKLLNEENKV LASQIREMKK LLETEDERAM  180
SPENSSSNNP PETLRLLK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A4e-19181180MEF2C
5f28_B4e-19181180MEF2C
5f28_C4e-19181180MEF2C
5f28_D4e-19181180MEF2C
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor involved in the negative regulation of flowering time in short days, probably through the photoperiodic and vernalization pathways. Prevents premature flowering, particularly in the cv. Landsberg erecta background. In non-inductive photoperiods (e.g. short days), required for flowering through VIL2-mediated maintenance of the epigenetically repressed state of MAF5 via H3K9me2 and plant homeodomain / polycomb repressive complex 2 (PHD-PRC2)-dependent H3K27me3. {ECO:0000269|PubMed:12724541, ECO:0000269|PubMed:18798874, ECO:0000269|PubMed:18852898, ECO:0000269|PubMed:20837520, ECO:0000269|PubMed:21150261, ECO:0000269|PubMed:21175890, ECO:0000269|PubMed:21398257, ECO:0000269|PubMed:22378382}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCsa18g038770.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated by vernalization. Repressed by VIL2, AGL6, CLF, EMF2 and FIE via epigenetic chromatin H3K27me3 and H3K9me2 regulation during the vegetative development. {ECO:0000269|PubMed:12724541}.
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_010484311.11e-141PREDICTED: protein MADS AFFECTING FLOWERING 5-like
SwissprotQ683D71e-95MAF5_ARATH; Protein MADS AFFECTING FLOWERING 5
TrEMBLV4KN533e-99V4KN53_EUTSA; Uncharacterized protein
STRINGXP_010484311.11e-140(Camelina sativa)
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
AT5G65070.17e-89MIKC_MADS family protein
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. 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]
  3. Xu Y,Gan ES,Ito T
    The AT-hook/PPC domain protein TEK negatively regulates floral repressors including MAF4 and MAF5.
    Plant Signal Behav, 2014.
    [PMID:23733063]
  4. Liu B, et al.
    Interplay of the histone methyltransferases SDG8 and SDG26 in the regulation of transcription and plant flowering and development.
    Biochim. Biophys. Acta, 2016. 1859(4): p. 581-90
    [PMID:26854085]
  5. Gong X,Shen L,Peng YZ,Gan Y,Yu H
    DNA Topoisomerase Iα Affects the Floral Transition.
    Plant Physiol., 2017. 173(1): p. 642-654
    [PMID:27837087]
  6. Cui Z, et al.
    SKIP controls flowering time via the alternative splicing of SEF pre-mRNA in Arabidopsis.
    BMC Biol., 2017. 15(1): p. 80
    [PMID:28893254]