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 GSBRNA2T00106863001
Common NameGSBRNA2T00106863001
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: 220aa    MW: 25052.7 Da    PI: 10.1015
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00106863001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF90.77.3e-29959151
                         S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
               SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                         krien + rqvtfskRrng+lKKA+ELSvLCdaev +iifs++ klye+ss
  GSBRNA2T00106863001  9 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVGLIIFSPRSKLYEFSS 59
                         79***********************************************96 PP
2K-box77.14.4e-2679170898
                K-box   8 s.leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrk 96 
                          + + e+++++ + e   L k+ie+L  ++R+llG++++ +s++eLqqLe+qLe++l++iR+kK++ll+e+ie+l++ e++l +enk+L++
  GSBRNA2T00106863001  79 NhTRENNSQQARDETYGLTKKIEQLDISKRKLLGKGIDACSIEELQQLENQLERGLSRIRAKKYQLLREEIEKLKEEERNLIKENKELKE 168
                          34789999*********************************************************************************9 PP

                K-box  97 kl 98 
                          k+
  GSBRNA2T00106863001 169 KW 170
                          97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006631.357161IPR002100Transcription factor, MADS-box
SMARTSM004321.5E-39160IPR002100Transcription factor, MADS-box
CDDcd002651.07E-40371No hitNo description
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004044.7E-30323IPR002100Transcription factor, MADS-box
SuperFamilySSF554552.22E-32386IPR002100Transcription factor, MADS-box
PfamPF003191.2E-251057IPR002100Transcription factor, MADS-box
PRINTSPR004044.7E-302338IPR002100Transcription factor, MADS-box
PRINTSPR004044.7E-303859IPR002100Transcription factor, MADS-box
PfamPF014861.8E-2482170IPR002487Transcription factor, K-box
PROSITE profilePS5129714.52886176IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010048Biological Processvernalization response
GO:0048510Biological Processregulation of timing of transition from vegetative to reproductive phase
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: 220 aa     Download sequence    Send to blast
MVRGKTEIKR IENATSRQVT FSKRRNGLLK KAFELSVLCD AEVGLIIFSP RSKLYEFSSS  60
SIAKTIERYQ KRVKETGINH TRENNSQQAR DETYGLTKKI EQLDISKRKL LGKGIDACSI  120
EELQQLENQL ERGLSRIRAK KYQLLREEIE KLKEEERNLI KENKELKEKW RGMGAIVVAS  180
PSSTLSSAEV NTDSVDNMEV ETGLFIGPPE PRQSKKLPL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A3e-18169169MEF2C
5f28_B3e-18169169MEF2C
5f28_C3e-18169169MEF2C
5f28_D3e-18169169MEF2C
Search in ModeBase
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
PlantRegMapGSBRNA2T00106863001
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF3126640.0AF312664.1 Arabidopsis thaliana MADS-box protein AGL19 (AGL19) mRNA, complete cds.
GenBankAY1425230.0AY142523.1 Arabidopsis thaliana putative MADS box AGL protein (At4g22950) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_022572578.11e-156agamous-like MADS-box protein AGL19
SwissprotO827431e-127AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBLA0A398A4L71e-155A0A398A4L7_BRACM; Uncharacterized protein
STRINGBra019343.1-P1e-155(Brassica rapa)
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-100AGAMOUS-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. 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]