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 Csa16g041240.1
Organism
Camelina sativa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Camelina
Family MIKC_MADS
Protein Properties Length: 185aa    MW: 20957 Da    PI: 9.6554
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Csa16g041240.1genomeCSGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF64.61e-20956148
                    S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEE CS
          SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklye 48
                    krienks rqvtfskRr g++ KA  LS+LC+  +av+++s +gkly 
  Csa16g041240.1  9 KRIENKSSRQVTFSKRRSGLIDKARQLSILCESSIAVVVVSASGKLYN 56
                    79********************************************97 PP
2K-box33.41.9e-12951632997
           K-box  29 enLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkk 97 
                     e L+  q +l+  ++++ s+  L +Le+qL ++l+  R++K+el++++++ lq+ke  l+een+ L ++
  Csa16g041240.1  95 ELLEMVQSKLVEPNVDNVSVDFLISLEEQLATALSISRARKTELMIASVKSLQEKEMLLREENHVLASQ 163
                     56677777788888999999********************************************99876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004322.1E-31160IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.19E-24171IPR002100Transcription factor, MADS-box
PROSITE profilePS5006627.572161IPR002100Transcription factor, MADS-box
CDDcd002655.51E-31270No hitNo description
PRINTSPR004041.1E-22323IPR002100Transcription factor, MADS-box
PfamPF003191.3E-201055IPR002100Transcription factor, MADS-box
PRINTSPR004041.1E-222338IPR002100Transcription factor, MADS-box
PRINTSPR004041.1E-223859IPR002100Transcription factor, MADS-box
PROSITE profilePS512979.91680170IPR002487Transcription factor, K-box
PfamPF014868.4E-995163IPR002487Transcription 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: 185 aa     Download sequence    Send to blast
MGRRKIEIKR IENKSSRQVT FSKRRSGLID KARQLSILCE SSIAVVVVSA SGKLYNSSSG  60
EDMSQIIERY DIQHADELKA LDLAEKTRNY LPHKELLEMV QSKLVEPNVD NVSVDFLISL  120
EEQLATALSI SRARKTELMI ASVKSLQEKE MLLREENHVL ASQKKRNVRK FLTDGEEHVY  180
GNRG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6byy_A6e-16170169MEF2 CHIMERA
6byy_B6e-16170169MEF2 CHIMERA
6byy_C6e-16170169MEF2 CHIMERA
6byy_D6e-16170169MEF2 CHIMERA
6bz1_A6e-16170169MEF2 CHIMERA
6bz1_B6e-16170169MEF2 CHIMERA
6bz1_C6e-16170169MEF2 CHIMERA
6bz1_D6e-16170169MEF2 CHIMERA
Search in ModeBase
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
PlantRegMapCsa16g041240.1
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
GenBankKU9368241e-172KU936824.1 Arabidopsis thaliana clone NSF1 flowering locus M splice variant (FLM) mRNA, partial sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010471874.11e-131PREDICTED: agamous-like MADS-box protein AGL27 isoform X2
SwissprotQ9LSR74e-89AGL70_ARATH; Agamous-like MADS-box protein AGL70
TrEMBLE4MW802e-89E4MW80_EUTHA; mRNA, clone: RTFL01-07-K22
STRINGXP_010471873.11e-112(Camelina sativa)
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
AT1G77080.46e-87MIKC_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]