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_013614580.1
Organism
Brassica oleracea
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 M-type_MADS
Protein Properties Length: 192aa    MW: 22060.7 Da    PI: 9.8348
Description M-type_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_013614580.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF76.32.3e-24956148
                    S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEE CS
          SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklye 48
                    krienks rqvtf+kRrng++KKA  LSvLC+  va++i+sstgkly 
  XP_013614580.1  9 KRIENKSSRQVTFCKRRNGLMKKARQLSVLCESSVALLIVSSTGKLYS 56
                    79********************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006628.567161IPR002100Transcription factor, MADS-box
SMARTSM004321.4E-33160IPR002100Transcription factor, MADS-box
SuperFamilySSF554555.89E-27173IPR002100Transcription factor, MADS-box
CDDcd002651.05E-31271No hitNo description
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004044.1E-24323IPR002100Transcription factor, MADS-box
PfamPF003196.9E-231056IPR002100Transcription factor, MADS-box
PRINTSPR004044.1E-242338IPR002100Transcription factor, MADS-box
PRINTSPR004044.1E-243859IPR002100Transcription factor, MADS-box
PROSITE profilePS512977.69880188IPR002487Transcription 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: 192 aa     Download sequence    Send to blast
MGRRKAEIKR IENKSSRQVT FCKRRNGLMK KARQLSVLCE SSVALLIVSS TGKLYSSSSG  60
DSMAKILKRY EIQHADELKT VDLAEKGRSY LSHEELLEIV QCKLEEAKSD NISVESLISL  120
EEQFKSAQSI TRAGKNMLWT LLVFGSCFQF DKFLNLMMEL VKTLQEKEKL LREENKVLAS  180
QLTKMEKNRF LE
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A2e-17170169MEF2C
5f28_B2e-17170169MEF2C
5f28_C2e-17170169MEF2C
5f28_D2e-17170169MEF2C
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_013614580.1
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013614580.11e-135PREDICTED: protein MADS AFFECTING FLOWERING 5-like
SwissprotQ9LSR75e-74AGL70_ARATH; Agamous-like MADS-box protein AGL70
TrEMBLA0A078H0K51e-99A0A078H0K5_BRANA; BnaA02g34550D protein
STRINGBra031884.1-P1e-100(Brassica rapa)
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
AT5G65070.14e-73MIKC_MADS family protein
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]