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 Rsa1.0_00070.1_g00005.1
Organism
Raphanus sativus
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: 233aa    MW: 26552.2 Da    PI: 8.2005
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_00070.1_g00005.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF88.14.9e-282171151
                             S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
                   SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                             k+i+n + rqvtfskRr gi+KKA ELSvLCda+va+iifs tgkl+e+ss
  Rsa1.0_00070.1_g00005.1 21 KKIDNITARQVTFSKRRRGIFKKADELSVLCDADVALIIFSATGKLFEFSS 71
                             68***********************************************96 PP
2K-box62.71.4e-21991831498
                    K-box  14 aeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                              ++  + ++++L +e+e   +++R+l GedLe L+l+eLq+Le+ Le++l+++ +kK e+l+++i+ l k+  el +enk+Lr+++
  Rsa1.0_00070.1_g00005.1  99 HQVEDCNVSRLSQEVEDKTKQLRKLRGEDLEGLNLEELQRLEKLLESGLSRVSEKKGEFLMSEISSLEKRGSELVDENKRLRERV 183
                              666677899*************************************************************************976 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004323.6E-361372IPR002100Transcription factor, MADS-box
SuperFamilySSF554554.84E-291383IPR002100Transcription factor, MADS-box
PROSITE profilePS5006628.6791373IPR002100Transcription factor, MADS-box
CDDcd002656.27E-351481No hitNo description
PROSITE patternPS0035001569IPR002100Transcription factor, MADS-box
PRINTSPR004049.7E-251535IPR002100Transcription factor, MADS-box
PfamPF003198.8E-252269IPR002100Transcription factor, MADS-box
PRINTSPR004049.7E-253550IPR002100Transcription factor, MADS-box
PRINTSPR004049.7E-255071IPR002100Transcription factor, MADS-box
PROSITE profilePS5129713.57399189IPR002487Transcription factor, K-box
PfamPF014861.3E-19103183IPR002487Transcription 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: 233 aa     Download sequence    Send to blast
MGRQDSRSIV KEMAREKRRI KKIDNITARQ VTFSKRRRGI FKKADELSVL CDADVALIIF  60
SATGKLFEFS SSRMRDILGR YNLHASNINK VMGQPSPYHQ VEDCNVSRLS QEVEDKTKQL  120
RKLRGEDLEG LNLEELQRLE KLLESGLSRV SEKKGEFLMS EISSLEKRGS ELVDENKRLR  180
ERVVTMEMAK TMALKESVET ESATTNVSSY ESGAPPEDDF SDTSLKLGLP SWE
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A3e-171381169MEF2C
5f28_B3e-171381169MEF2C
5f28_C3e-171381169MEF2C
5f28_D3e-171381169MEF2C
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
11637KRRIKKIDNITARQVTFSKRRR
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator that mediates floral transition in response to vernalization. Promotes inflorescence fate in apical meristems. Acts in a dosage-dependent manner. Probably involved in the transduction of RLK-mediated signaling (e.g. IMK3 pathway). Together with AP1 and SVP, controls the identity of the floral meristem and regulates expression of class B, C and E genes. When associated with SOC1, mediates effect of gibberellins on flowering under short-day conditions, and regulates the expression of LEAFY (LFY), which links floral induction and floral development. Confers inflorescence characteristics to floral primordia and early flowering. {ECO:0000269|PubMed:12451184, ECO:0000269|PubMed:12609028, ECO:0000269|PubMed:12881501, ECO:0000269|PubMed:14716314, ECO:0000269|PubMed:16679456, ECO:0000269|PubMed:18339670, ECO:0000269|PubMed:18466303, ECO:0000269|PubMed:18694458, ECO:0000269|PubMed:19656343}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_00070.1_g00005.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Induced by vernalization in a FLC-independent manner. Repressed by the floral homeotic genes AP1, LFY and SEP3 in emerging floral meristems to establish a floral identity and prevent inflorescence fate. Up-regulated at the shoot apex by SOC1. {ECO:0000269|PubMed:12609028, ECO:0000269|PubMed:14716314, ECO:0000269|PubMed:17428825, ECO:0000269|PubMed:18339670, 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
GenBankJQ9067070.0JQ906707.1 Brassica napus clone AGL24-1 MADS-box protein AGL24 (AGL24) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013737984.11e-155MADS-box protein AGL24-like isoform X2
SwissprotO827941e-130AGL24_ARATH; MADS-box protein AGL24
TrEMBLA0A0D3DFW01e-157A0A0D3DFW0_BRAOL; Uncharacterized protein
STRINGBo7g109590.11e-158(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM145111521
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G24540.11e-113AGAMOUS-like 24
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. Lei HJ, et al.
    Identification and characterization of FaSOC1, a homolog of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 from strawberry.
    Gene, 2013. 531(2): p. 158-67
    [PMID:24055423]
  3. 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]
  4. Sacharowski SP, et al.
    SWP73 Subunits of Arabidopsis SWI/SNF Chromatin Remodeling Complexes Play Distinct Roles in Leaf and Flower Development.
    Plant Cell, 2015. 27(7): p. 1889-906
    [PMID:26106148]
  5. Sun LM,Zhang JZ,Hu CG
    Characterization and Expression Analysis of PtAGL24, a SHORT VEGETATIVE PHASE/AGAMOUS-LIKE 24 (SVP/AGL24)-Type MADS-Box Gene from Trifoliate Orange (Poncirus trifoliata L. Raf.).
    Front Plant Sci, 2016. 7: p. 823
    [PMID:27375669]