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_009140365.1
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: 241aa    MW: 27264.6 Da    PI: 5.8159
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009140365.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF89.71.5e-281059251
                    ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
          SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                    +i+n + rqvtfskRr g++KKAeELSvLCda+va+i+fsstgkl+e++s
  XP_009140365.1 10 KIDNATARQVTFSKRRRGLFKKAEELSVLCDADVALIVFSSTGKLFEFCS 59
                    69**********************************************96 PP
2K-box51.35.1e-18941702197
           K-box  21 lakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkk 97 
                      ++L kei    +++R++ Ge+L+ L+++eLqqLe++Le +l+++ ++K+e ++++i++lq+k  +l +enk+Lr+ 
  XP_009140365.1  94 NSRLSKEIADKSHQLRQMRGEELQGLNIEELQQLEKALEAGLTRVIETKSEKIMSEISDLQRKGMKLMDENKRLRQH 170
                     5789999999999*************************************************************985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004323.1E-40160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006630.291161IPR002100Transcription factor, MADS-box
CDDcd002651.45E-39277No hitNo description
PRINTSPR004043.7E-27323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
SuperFamilySSF554553.4E-31376IPR002100Transcription factor, MADS-box
PfamPF003193.4E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004043.7E-272338IPR002100Transcription factor, MADS-box
PRINTSPR004043.7E-273859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129713.38187180IPR002487Transcription factor, K-box
PfamPF014869.0E-1793169IPR002487Transcription 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: 241 aa     Download sequence    Send to blast
MAREKIQIRK IDNATARQVT FSKRRRGLFK KAEELSVLCD ADVALIVFSS TGKLFEFCSS  60
SMREVLERHN LQSKNLEKLD QPSLELQLVE NSDNSRLSKE IADKSHQLRQ MRGEELQGLN  120
IEELQQLEKA LEAGLTRVIE TKSEKIMSEI SDLQRKGMKL MDENKRLRQH GTQLTEENER  180
LGKQIYNNMH ERYGGVESEK TAVYEEGQSS ESITNAGNST GAPVDSESSD TSLRLGLPYG  240
G
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A4e-20169169MEF2C
5f28_B4e-20169169MEF2C
5f28_C4e-20169169MEF2C
5f28_D4e-20169169MEF2C
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.175890.0root
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: During vegetative phase expressed in young leaves and apical meristem until early stage of bolting. Early in development of the inflorescence present in the coflorescence and flower primordia but not in the main apical meristem. Present throughout the floral meristem during early stages of flower development. Later disappears prior to emergence of sepal primordia. {ECO:0000269|PubMed:19656343}.
UniprotTISSUE SPECIFICITY: Detected in roots and leaves. Expressed at very low levels in flowers and siliques. Present in floral meristems. {ECO:0000269|PubMed:19656343}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription repressor that inhibit floral transition in the autonomous flowering pathway, independent of photoperiod and temperature. Acts in a dosage-dependent manner. Together with AGL24 and AP1, controls the identity of the floral meristem and regulates expression of class B, C and E genes. Promotes EFM expression to suppress flowering (PubMed:25132385). {ECO:0000269|PubMed:16679456, ECO:0000269|PubMed:18694458, ECO:0000269|PubMed:19656343, ECO:0000269|PubMed:25132385}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009140365.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Repressed by the floral homeotic genes AP1 and SEP3 in emerging floral meristems. Up-regulated by HUA2. {ECO:0000269|PubMed:15659097, ECO:0000269|PubMed:17428825, ECO:0000269|PubMed:18694458}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankDQ6416750.0DQ641675.1 Brassica rapa subsp. campestris cultivar Jangmi short vegetative phase protein (SVP) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009140365.11e-175PREDICTED: MADS-box protein SVP isoform X2
SwissprotQ9FVC11e-158SVP_ARATH; MADS-box protein SVP
TrEMBLA0SMV61e-174A0SMV6_BRARO; Short vegetative phase protein
STRINGBo4g149800.11e-172(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM41902747
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G22540.11e-149MIKC_MADS family protein
Publications ? help Back to Top
  1. Ramamoorthy R,Phua EE,Lim SH,Tan HT,Kumar PP
    Identification and characterization of RcMADS1, an AGL24 ortholog from the holoparasitic plant Rafflesia cantleyi Solms-Laubach (Rafflesiaceae).
    PLoS ONE, 2013. 8(6): p. e67243
    [PMID:23840638]
  2. Jaudal M, et al.
    Overexpression of Medicago SVP genes causes floral defects and delayed flowering in Arabidopsis but only affects floral development in Medicago.
    J. Exp. Bot., 2014. 65(2): p. 429-42
    [PMID:24249713]
  3. Müller-Xing R,Clarenz O,Pokorny L,Goodrich J,Schubert D
    Polycomb-Group Proteins and FLOWERING LOCUS T Maintain Commitment to Flowering in Arabidopsis thaliana.
    Plant Cell, 2014. 26(6): p. 2457-2471
    [PMID:24920331]
  4. Hwan Lee J,Sook Chung K,Kim SK,Ahn JH
    Post-translational regulation of SHORT VEGETATIVE PHASE as a major mechanism for thermoregulation of flowering.
    Plant Signal Behav, 2014. 9(4): p. e28193
    [PMID:25764420]
  5. Chen Z, et al.
    Overexpression of AtAP1M3 regulates flowering time and floral development in Arabidopsis and effects key flowering-related genes in poplar.
    Transgenic Res., 2015. 24(4): p. 705-15
    [PMID:25820621]
  6. Wells CE,Vendramin E,Jimenez Tarodo S,Verde I,Bielenberg DG
    A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch].
    BMC Plant Biol., 2015. 15: p. 41
    [PMID:25848674]
  7. Müller-Xing R,Schubert D,Goodrich J
    Non-inductive conditions expose the cryptic bract of flower phytomeres in Arabidopsis thaliana.
    Plant Signal Behav, 2015. 10(4): p. e1010868
    [PMID:25924005]
  8. Marín-González E, et al.
    SHORT VEGETATIVE PHASE Up-Regulates TEMPRANILLO2 Floral Repressor at Low Ambient Temperatures.
    Plant Physiol., 2015. 169(2): p. 1214-24
    [PMID:26243615]
  9. Bechtold U, et al.
    Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis.
    Plant Cell, 2016. 28(2): p. 345-66
    [PMID:26842464]
  10. Fernández V,Takahashi Y,Le Gourrierec J,Coupland G
    Photoperiodic and thermosensory pathways interact through CONSTANS to promote flowering at high temperature under short days.
    Plant J., 2016. 86(5): p. 426-40
    [PMID:27117775]
  11. Wilson DC,Kempthorne CJ,Carella P,Liscombe DK,Cameron RK
    Age-Related Resistance in Arabidopsis thaliana Involves the MADS-Domain Transcription Factor SHORT VEGETATIVE PHASE and Direct Action of Salicylic Acid on Pseudomonas syringae.
    Mol. Plant Microbe Interact., 2017. 30(11): p. 919-929
    [PMID:28812948]
  12. Zou YP, et al.
    Adaptation of Arabidopsis thaliana to the Yangtze River basin.
    Genome Biol., 2017. 18(1): p. 239
    [PMID:29284515]
  13. Richter R, et al.
    Floral regulators FLC and SOC1 directly regulate expression of the B3-type transcription factor TARGET OF FLC AND SVP 1 at the Arabidopsis shoot apex via antagonistic chromatin modifications.
    PLoS Genet., 2019. 15(4): p. e1008065
    [PMID:30946745]