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 Carubv10028173m
Common NameCARUB_v10028173mg
Organism
Capsella rubella
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family MIKC_MADS
Protein Properties Length: 198aa    MW: 22552.9 Da    PI: 9.2299
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10028173mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF70.31.7e-22959151
                     S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
           SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                     krie+ks rqvtf+kRrng++ KA  LS+LC+  va++i+sst kly +ss
  Carubv10028173m  9 KRIEDKSSRQVTFCKRRNGLMEKARQLSILCESSVALVIVSSTRKLYSFSS 59
                     79***********************************************96 PP
2K-box34.11.2e-121111644598
            K-box  45 sLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                      + s+  L++Le+qL+++l+  R++K+el++e +++ q+kek l+een+ L+++l
  Carubv10028173m 111 NVSIDFLKSLEEQLKTALSVTRDRKTELMMEFVKTHQEKEKLLREENQILTSQL 164
                      667888********************************************9987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004328.6E-31160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006628.385161IPR002100Transcription factor, MADS-box
SuperFamilySSF554555.1E-26172IPR002100Transcription factor, MADS-box
CDDcd002657.03E-31277No hitNo description
PRINTSPR004041.9E-23323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003198.9E-221057IPR002100Transcription factor, MADS-box
PRINTSPR004041.9E-232338IPR002100Transcription factor, MADS-box
PRINTSPR004041.9E-233859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129710.48280170IPR002487Transcription factor, K-box
PfamPF014863.5E-9105164IPR002487Transcription 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: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: 198 aa     Download sequence    Send to blast
MGRRKVEIKR IEDKSSRQVT FCKRRNGLME KARQLSILCE SSVALVIVSS TRKLYSFSSG  60
DSMAKILSRF EVQQADDTKT SDLAETSRNY LSHKELLEIV QCKLEEAKSD NVSIDFLKSL  120
EEQLKTALSV TRDRKTELMM EFVKTHQEKE KLLREENQIL TSQLSKMKKS LETEDVRGVS  180
PESSCGKNTP ETLLLLK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A2e-19185186MEF2C
5f28_B2e-19185186MEF2C
5f28_C2e-19185186MEF2C
5f28_D2e-19185186MEF2C
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
PlantRegMapCarubv10028173m
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY2314501e-163AY231450.1 Arabidopsis thaliana MADS affecting flowering 4 variant I (MAF4) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006279830.11e-139protein MADS AFFECTING FLOWERING 5 isoform X1
SwissprotQ683D75e-88MAF5_ARATH; Protein MADS AFFECTING FLOWERING 5
TrEMBLR0GNG31e-138R0GNG3_9BRAS; Uncharacterized protein
STRINGXP_006279830.11e-138(Capsella rubella)
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
AT5G65070.11e-113MIKC_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]