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_009136496.1
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: 221aa    MW: 25099.7 Da    PI: 9.7417
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009136496.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF93.11.4e-29959151
                    S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
          SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                    krien + rqvtfskRrng+lKKA+ELSvLCdaeva+iifs++ klye+ss
  XP_009136496.1  9 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPSSKLYEFSS 59
                    79***********************************************96 PP
2K-box79.58e-2779170898
           K-box   8 s.leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                     + + + ++++ + e   L k+ie+L+ ++R+llGe+++ +s++eLqqLe+qLe++l++iR+kK++ll+e+ie+l++ e++l +enk+L++kl
  XP_009136496.1  79 NhKRDDNSQQAKGETYGLTKKIEQLEISKRKLLGEGIDACSIEELQQLENQLERGLTRIRAKKYQLLREEIEKLKEEERNLIKENKELKEKL 170
                     3477889999*******************************************************************************997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006631.413161IPR002100Transcription factor, MADS-box
SMARTSM004324.4E-40160IPR002100Transcription factor, MADS-box
CDDcd002651.45E-40370No hitNo description
PRINTSPR004045.6E-30323IPR002100Transcription factor, MADS-box
SuperFamilySSF554552.88E-32383IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003191.8E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004045.6E-302338IPR002100Transcription factor, MADS-box
PRINTSPR004045.6E-303859IPR002100Transcription factor, MADS-box
PfamPF014861.2E-2582170IPR002487Transcription factor, K-box
PROSITE profilePS5129715.19786176IPR002487Transcription 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: 221 aa     Download sequence    Send to blast
MVRGKTEMKR IENATSRQVT FSKRRNGLLK KAFELSVLCD AEVALIIFSP SSKLYEFSSS  60
GIAKTIERYQ RRVKETGVNH KRDDNSQQAK GETYGLTKKI EQLEISKRKL LGEGIDACSI  120
EELQQLENQL ERGLTRIRAK KYQLLREEIE KLKEEERNLI KENKELKEKL HGMGAIVVAS  180
SSSTLSSAEV NMDDNGNMEV ETGLFIGPPE TRQSKKIPPQ N
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6byy_A6e-19169169MEF2 CHIMERA
6byy_B6e-19169169MEF2 CHIMERA
6byy_C6e-19169169MEF2 CHIMERA
6byy_D6e-19169169MEF2 CHIMERA
6bz1_A6e-19169169MEF2 CHIMERA
6bz1_B6e-19169169MEF2 CHIMERA
6bz1_C6e-19169169MEF2 CHIMERA
6bz1_D6e-19169169MEF2 CHIMERA
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.190150.0bud
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Mostly expressed in the outer layers of the root meristem (lateral root cap and epidermis) and in the central cylinder cells of mature roots. Also present in rosette leaves and seedlings and, to a lesser extent, in cauline leaves and flowers. Enriched in apices including the shoot apical meristem and developing leaf primordia. {ECO:0000269|PubMed:11115127, ECO:0000269|PubMed:12837945, ECO:0000269|PubMed:12949148, ECO:0000269|PubMed:16778081}.
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009136496.1
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009136496.11e-159PREDICTED: agamous-like MADS-box protein AGL19
SwissprotO827431e-131AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBLA0A398ALC21e-157A0A398ALC2_BRACM; Uncharacterized protein
STRINGBo1g031900.11e-139(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM7828413
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G22950.11e-103AGAMOUS-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]