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 XP_009130488.1
Organism
Brassica rapa
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: 199aa    MW: 22917.4 Da    PI: 8.8705
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009130488.1genomeNCBIView 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+
  XP_009130488.1  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
  XP_009130488.1 110 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: 199 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
PlantRegMapXP_009130488.1
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. 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]
  3. 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]