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 RrC7998_p1
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family MIKC_MADS
Protein Properties Length: 237aa    MW: 27004.2 Da    PI: 5.279
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC7998_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF87.29e-281057249
                ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEE CS
      SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyey 49
                +i+n + rqvtfskRr g++KKAeELSvLCda+va+i+fsstgkl+e+
  RrC7998_p1 10 KIDNATARQVTFSKRRRGLFKKAEELSVLCDADVALIVFSSTGKLFEF 57
                69*********************************************9 PP
2K-box523.1e-18861632097
       K-box  20 elakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkk 97 
                 + a+L kei    +++R++ Ge+L+ L+++eLqqLe++Le +l+++  +K+e ++++i++lq+k  +l +enk+Lr++
  RrC7998_p1  86 DNARLSKEIADKSHQLRQMRGEELQGLNIEELQQLEKALEAGLSRVIGTKSEKIMNEISDLQRKGMQLMDENKRLRQQ 163
                 5689999999999***************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004322.0E-37160IPR002100Transcription factor, MADS-box
SuperFamilySSF554558.37E-27162IPR002100Transcription factor, MADS-box
PROSITE profilePS5006629.24161IPR002100Transcription factor, MADS-box
CDDcd002651.74E-33270No hitNo description
PRINTSPR004046.6E-26323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003193.3E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004046.6E-262338IPR002100Transcription factor, MADS-box
PRINTSPR004046.6E-263859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129713.65880173IPR002487Transcription factor, K-box
PfamPF014862.1E-1786163IPR002487Transcription factor, K-box
Gene3DG3DSA:1.20.5.1703.7E-4141180No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009266Biological Processresponse to temperature stimulus
GO:0009910Biological Processnegative regulation of flower development
GO:0010076Biological Processmaintenance of floral meristem identity
GO:0010582Biological Processfloral meristem determinacy
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048438Biological Processfloral whorl development
GO:0005634Cellular Componentnucleus
GO:0000900Molecular Functiontranslation repressor activity, nucleic acid binding
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: 237 aa     Download sequence    Send to blast
MAREKIQIRK IDNATARQVT FSKRRRGLFK KAEELSVLCD ADVALIVFSS TGKLFEFLLE  60
RHNLQSKNLE KLDQPSLELQ LVENSDNARL SKEIADKSHQ LRQMRGEELQ GLNIEELQQL  120
EKALEAGLSR VIGTKSEKIM NEISDLQRKG MQLMDENKRL RQQGTQLTEE NERLGEQVSR  180
YYFEHIYNNM HERYGGVESE NTAVYEEGHS SESITNAGNS TGAPVDSESS DTSLRLG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A2e-17157157MEF2C
5f28_B2e-17157157MEF2C
5f28_C2e-17157157MEF2C
5f28_D2e-17157157MEF2C
Search in ModeBase
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00272DAPTransfer from AT2G22540Download
Motif logo
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
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankDQ6416751e-166DQ641675.1 Brassica rapa subsp. campestris cultivar Jangmi short vegetative phase protein (SVP) mRNA, complete cds.
GenBankJQ9067161e-166JQ906716.1 Brassica juncea clone SVP-2 MADS-box protein SVP (SVP) mRNA, complete cds.
GenBankJQ9067181e-166JQ906718.1 Brassica napus clone SVP-2 MADS-box protein SVP (SVP) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018484701.11e-158PREDICTED: MADS-box protein SVP-like
RefseqXP_018485055.11e-158PREDICTED: MADS-box protein SVP-like
SwissprotQ9FVC11e-142SVP_ARATH; MADS-box protein SVP
TrEMBLI6TF571e-151I6TF57_BRANA; MADS-box protein SVP
STRINGBra030228.1-P1e-151(Brassica rapa)
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-132MIKC_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]