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 RrC11244_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: 150aa    MW: 16943.7 Da    PI: 9.4766
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC11244_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF83.11.8e-26957149
                 S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEE CS
       SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyey 49
                 krien   rqvtf+kRr+g+lKKA+ELSvLCdae+ v+ifs++gkl+e 
  RrC11244_p1  9 KRIENPVHRQVTFCKRRTGLLKKAKELSVLCDAEIGVVIFSPQGKLFEL 57
                 79********************************************996 PP
2K-box34.49.6e-13911501069
        K-box  10 eeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskK 69 
                   + ++   + e++ Lk+eie+Lq+ +R + G + + ++l+eL  Le++Le  +++iRs K
  RrC11244_p1  91 LKPQNHDPKDEVNVLKQEIEMLQKGIRYRFGGGEGAMNLEELLLLEKHLEYWISQIRSAK 150
                  4555667899***********************************************987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004321.1E-36160IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.44E-28174IPR002100Transcription factor, MADS-box
PROSITE profilePS5006629.506161IPR002100Transcription factor, MADS-box
CDDcd002651.97E-38372No hitNo description
PRINTSPR004048.1E-28323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003192.5E-241056IPR002100Transcription factor, MADS-box
PRINTSPR004048.1E-282338IPR002100Transcription factor, MADS-box
PRINTSPR004048.1E-283859IPR002100Transcription factor, MADS-box
PfamPF014865.3E-1194150IPR002487Transcription factor, K-box
PROSITE profilePS512978.62295150IPR002487Transcription 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: 150 aa     Download sequence    Send to blast
MVRGKIQLKR IENPVHRQVT FCKRRTGLLK KAKELSVLCD AEIGVVIFSP QGKLFELATK  60
GTMEGVIDKY MKCTSGGCSS SSATYTAQEQ LKPQNHDPKD EVNVLKQEIE MLQKGIRYRF  120
GGGEGAMNLE ELLLLEKHLE YWISQIRSAK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
3mu6_A3e-17370268Myocyte-specific enhancer factor 2A
3mu6_B3e-17370268Myocyte-specific enhancer factor 2A
3mu6_C3e-17370268Myocyte-specific enhancer factor 2A
3mu6_D3e-17370268Myocyte-specific enhancer factor 2A
5f28_A5e-17170169MEF2C
5f28_B5e-17170169MEF2C
5f28_C5e-17170169MEF2C
5f28_D5e-17170169MEF2C
6byy_A4e-17170169MEF2 CHIMERA
6byy_B4e-17170169MEF2 CHIMERA
6byy_C4e-17170169MEF2 CHIMERA
6byy_D4e-17170169MEF2 CHIMERA
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
GenBankAK2281901e-168AK228190.1 Arabidopsis thaliana mRNA for MADS-box protein AGL12, complete cds, clone: RAFL14-63-K22.
GenBankATU201931e-168U20193.1 Arabidopsis thaliana MADS-box protein AGL12 (AGL12) mRNA, complete cds.
GenBankBT0061571e-168BT006157.1 Arabidopsis thaliana clone RAFL17-04-C08 (R50439) putative MADS-box protein (At1g71692) mRNA, complete cds.
GenBankBT0083321e-168BT008332.1 Arabidopsis thaliana At1g71692 gene, complete cds.
GenBankBT0085241e-168BT008524.1 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_018454918.11e-108PREDICTED: agamous-like MADS-box protein AGL12
SwissprotQ388415e-88AGL12_ARATH; Agamous-like MADS-box protein AGL12
TrEMBLA0A1J3FTK67e-87A0A1J3FTK6_NOCCA; Agamous-like MADS-box protein AGL12
STRINGCagra.2418s0012.1.p6e-87(Capsella grandiflora)
STRINGXP_006300552.16e-87(Capsella rubella)
STRINGXP_010427993.16e-87(Camelina sativa)
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-78AGAMOUS-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]