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 GSBRNA2T00047454001
Common NameGSBRNA2T00047454001
Organism
Brassica napus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family MIKC_MADS
Protein Properties Length: 200aa    MW: 22917.4 Da    PI: 8.8705
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00047454001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF68.46.9e-22956148
                         S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEE CS
               SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklye 48
                         krie+ks rqvtf+kRrng++ KA  LSvLC+  va++++sstgkly+
  GSBRNA2T00047454001  9 KRIESKSSRQVTFCKRRNGLIEKARQLSVLCESSVAILMVSSTGKLYT 56
                         79*********************************************9 PP
2K-box325e-121101644498
                K-box  44 esLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                          ++ s++ L++Le+q + +l+  R++K++l++e +++l +kek l+een+ L ++l
  GSBRNA2T00047454001 110 DDASVESLNSLEEQFKAALSVTRARKTQLMMEFLKNLEEKEKLLREENQILASQL 164
                          5668999********************************************9987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004322.7E-29160IPR002100Transcription factor, MADS-box
SuperFamilySSF554554.58E-25173IPR002100Transcription factor, MADS-box
PROSITE profilePS5006626.871161IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004041.6E-21323IPR002100Transcription factor, MADS-box
PfamPF003191.6E-201056IPR002100Transcription factor, MADS-box
PRINTSPR004041.6E-212338IPR002100Transcription factor, MADS-box
PRINTSPR004041.6E-213859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129710.74570170IPR002487Transcription factor, K-box
PfamPF014867.9E-10109164IPR002487Transcription 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: 200 aa     Download sequence    Send to blast
MGRRKVEIKR IESKSSRQVT FCKRRNGLIE KARQLSVLCE SSVAILMVSS TGKLYTSSYG  60
DSMEKIIKRY EIQHADELKN LDLEEKFRKY LSYKELVDIV QCKCEEAKVD DASVESLNSL  120
EEQFKAALSV TRARKTQLMM EFLKNLEEKE KLLREENQIL ASQLTKMEKK RLPETEGEGA  180
MSSENSSRNS PPETLPLLK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A8e-15170169MEF2C
5f28_B8e-15170169MEF2C
5f28_C8e-15170169MEF2C
5f28_D8e-15170169MEF2C
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Mostly expressed in roots, leaves and flowers, and, to a lower extent, in inflorescence, siliques, pollen and shoots. {ECO:0000269|PubMed:12837945, ECO:0000269|PubMed:12949148}.
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapGSBRNA2T00047454001
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1667412e-98AC166741.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH080C09, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009130488.11e-141PREDICTED: protein MADS AFFECTING FLOWERING 5-like
SwissprotQ9LSR79e-87AGL70_ARATH; Agamous-like MADS-box protein AGL70
TrEMBLA0A078H1H31e-140A0A078H1H3_BRANA; BnaA02g34520D protein
TrEMBLA0A3G5BC801e-140A0A3G5BC80_BRARC; Maf-like protein
STRINGXP_006394081.11e-103(Eutrema salsugineum)
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
AT5G65050.38e-72AGAMOUS-like 31
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. Chalhoub B, et al.
    Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.
    Science, 2014. 345(6199): p. 950-3
    [PMID:25146293]
  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]