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 RrC1514_p2
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: 211aa    MW: 23981.6 Da    PI: 7.4354
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC1514_p2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF80.61e-25957149
                S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEE CS
      SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyey 49
                krien   rqvtf+kRr+g+lKKA+ELSvLCdae+ v+ifss+gkl+e 
  RrC1514_p2  9 KRIENPVHRQVTFCKRRTGLLKKAKELSVLCDAEIGVMIFSSQGKLFEL 57
                79********************************************996 PP
2K-box55.13.2e-1910118120100
       K-box  20 elakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkklee 100
                 +++ Lk+ei++Lq+ +  + G + e+++l+eL  Le+++e  +++iRs K+e++l++i+ l++ e  l+++nk+L +k+ee
  RrC1514_p2 101 QVNELKQEIDMLQKGISYMFGGGDETMNLQELILLEKHVEYWISHIRSAKMEIMLQEIQSLRNTEGVLKNANKYLLEKIEE 181
                 6899**************************************************************************997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF554553.14E-28175IPR002100Transcription factor, MADS-box
SMARTSM004321.6E-36160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006630.025161IPR002100Transcription factor, MADS-box
CDDcd002656.71E-40278No hitNo description
PRINTSPR004041.4E-27323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003198.9E-231056IPR002100Transcription factor, MADS-box
PRINTSPR004041.4E-272338IPR002100Transcription factor, MADS-box
PRINTSPR004041.4E-273859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129711.87395185IPR002487Transcription factor, K-box
PfamPF014868.9E-18101179IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0048364Biological Processroot development
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
MARGKIQLKR IENPVHRQVT FCKRRTGLLK KAKELSVLCD AEIGVMIFSS QGKLFELATK  60
GTMEGMIDKY MKCTNGGRGS SSATFTAQEQ LQPPNLDPKG QVNELKQEID MLQKGISYMF  120
GGGDETMNLQ ELILLEKHVE YWISHIRSAK MEIMLQEIQS LRNTEGVLKN ANKYLLEKIE  180
ENNNSVLDAN FTTVETNYSY PLTMPSETFQ F
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A1e-16170169MEF2C
5f28_B1e-16170169MEF2C
5f28_C1e-16170169MEF2C
5f28_D1e-16170169MEF2C
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription activator that regulates root development by controlling cell proliferation in root meristem. May mediate responses to auxin in the root. May act as promoter of the flowering transition through up-regulation of SOC, FT and LFY. {ECO:0000269|PubMed:18203871}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin in root phloem. {ECO:0000269|PubMed:18203871}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2281900.0AK228190.1 Arabidopsis thaliana mRNA for MADS-box protein AGL12, complete cds, clone: RAFL14-63-K22.
GenBankBT0061570.0BT006157.1 Arabidopsis thaliana clone RAFL17-04-C08 (R50439) putative MADS-box protein (At1g71692) mRNA, complete cds.
GenBankBT0083320.0BT008332.1 Arabidopsis thaliana At1g71692 gene, complete cds.
GenBankBT0085240.0BT008524.1 Arabidopsis thaliana clone U50439 putative MADS-box protein (At1g71692) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018444256.11e-140PREDICTED: agamous-like MADS-box protein AGL12
SwissprotQ388411e-132AGL12_ARATH; Agamous-like MADS-box protein AGL12
TrEMBLA0A0D3CXA41e-136A0A0D3CXA4_BRAOL; Uncharacterized protein
STRINGBo6g094120.11e-137(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM70522641
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G71692.11e-135AGAMOUS-like 12
Publications ? help Back to Top
  1. Zimmermann P,Hirsch-Hoffmann M,Hennig L,Gruissem W
    GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox.
    Plant Physiol., 2004. 136(1): p. 2621-32
    [PMID:15375207]
  2. Pacheco-Escobedo MA, et al.
    Longitudinal zonation pattern in Arabidopsis root tip defined by a multiple structural change algorithm.
    Ann. Bot., 2018.
    [PMID:27358290]
  3. García-Cruz KV, et al.
    The MADS-box XAANTAL1 increases proliferation at the Arabidopsis root stem-cell niche and participates in transition to differentiation by regulating cell-cycle components.
    Ann. Bot., 2018.
    [PMID:27474508]