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 Cagra.6745s0008.1.p
Organism
Capsella grandiflora
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: 211aa    MW: 24148.6 Da    PI: 9.8045
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.6745s0008.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF92.42.2e-29959151
                         S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
               SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                         krien + rqvtfskRrng+lKKA+ELSvLCdaeva++ifs++ klye+ss
  Cagra.6745s0008.1.p  9 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALVIFSPRSKLYEFSS 59
                         79***********************************************96 PP
2K-box80.54.1e-2781170998
                K-box   9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                          + +a++++ + e + L k+ie+L+ ++R+llGe+++++s++eLqqLe+qLe++l++iR+kK++ll+++ie+l++ e++l +enk+L++k+
  Cagra.6745s0008.1.p  81 KGDANSQQAKDETRVLTKKIEQLEISKRKLLGEGIDTCSIEELQQLENQLERGLTRIRAKKYQLLRAEIEKLKEEERKLAKENKELKEKW 170
                          678999*********************************************************************************996 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004323.5E-39160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006631.286161IPR002100Transcription factor, MADS-box
CDDcd002651.04E-39370No hitNo description
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
SuperFamilySSF554555.36E-32374IPR002100Transcription factor, MADS-box
PRINTSPR004044.0E-30323IPR002100Transcription factor, MADS-box
PfamPF003194.5E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004044.0E-302338IPR002100Transcription factor, MADS-box
PRINTSPR004044.0E-303859IPR002100Transcription factor, MADS-box
PfamPF014863.7E-2684169IPR002487Transcription factor, K-box
PROSITE profilePS5129715.02186176IPR002487Transcription 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: 211 aa     Download sequence    Send to blast
MVRGKTEMKR IENATSRQVT FSKRRNGLLK KAFELSVLCD AEVALVIFSP RSKLYEFSSS  60
SITKTIERYQ RRVKEIGINH KGDANSQQAK DETRVLTKKI EQLEISKRKL LGEGIDTCSI  120
EELQQLENQL ERGLTRIRAK KYQLLRAEIE KLKEEERKLA KENKELKEKW LGMGATVASS  180
QSTLSSSEVN IDDDNNMEVE TGLFIGPPET R
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A4e-18169169MEF2C
5f28_B4e-18169169MEF2C
5f28_C4e-18169169MEF2C
5f28_D4e-18169169MEF2C
Search in ModeBase
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
PlantRegMapCagra.6745s0008.1.p
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_023634924.11e-149agamous-like MADS-box protein AGL19
SwissprotO827431e-123AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBLR0F2Q81e-148R0F2Q8_9BRAS; Uncharacterized protein
STRINGCagra.6745s0008.1.p1e-150(Capsella grandiflora)
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-97AGAMOUS-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]