PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os03g11614.1
Common NameLHS1, LOC4332059, MADS1, Os03g0215400, OsJ_09913
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family MIKC_MADS
Protein Properties Length: 258aa    MW: 29528.2 Da    PI: 7.3445
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os03g11614.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF88.63.4e-28959151
                      S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
            SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                      krienk+ rqvtf+kRrng+lKKA+ELS LCdaeva+iifs +g+l+e+ss
  LOC_Os03g11614.1  9 KRIENKISRQVTFAKRRNGLLKKAYELSLLCDAEVALIIFSGRGRLFEFSS 59
                      79***********************************************96 PP

2K-box97.91.6e-32771716100
             K-box   6 gksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                       ++++++ ++e  +qe+ kLk ++e Lq++qR++lGedL++Ls+keL+qLe+q+e slk+iRs+Kn+ ll+q+ +l+ ke++lq+ nk+Lrkkl
  LOC_Os03g11614.1  77 SQDAAAPENEINYQEYLKLKTRVEFLQTTQRNILGEDLGPLSMKELEQLENQIEVSLKQIRSRKNQALLDQLFDLKSKEQQLQDLNKDLRKKL 169
                       4456777888999*******************************************************************************9 PP

             K-box  99 ee 100
                       +e
  LOC_Os03g11614.1 170 QE 171
                       87 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006632.52161IPR002100Transcription factor, MADS-box
SMARTSM004323.7E-39160IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.7E-32291IPR002100Transcription factor, MADS-box
CDDcd002652.35E-43279No hitNo description
PRINTSPR004045.8E-31323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003191.6E-241057IPR002100Transcription factor, MADS-box
PRINTSPR004045.8E-312338IPR002100Transcription factor, MADS-box
PRINTSPR004045.8E-313859IPR002100Transcription factor, MADS-box
PfamPF014868.5E-2784170IPR002487Transcription factor, K-box
PROSITE profilePS5129715.71285175IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010093Biological Processspecification of floral organ identity
GO:0010582Biological Processfloral meristem determinacy
GO:0030154Biological Processcell differentiation
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009038anatomypalea
PO:0001048developmental stagepalea development stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 258 aa     Download sequence    Send to blast
MGRGKVELKR IENKISRQVT FAKRRNGLLK KAYELSLLCD AEVALIIFSG RGRLFEFSSS  60
SCMYKTLERY RSCNYNSQDA AAPENEINYQ EYLKLKTRVE FLQTTQRNIL GEDLGPLSMK  120
ELEQLENQIE VSLKQIRSRK NQALLDQLFD LKSKEQQLQD LNKDLRKKLQ ETSAENVLHM  180
SWQDGGGHSG SSTVLADQPH HHQGLLHPHP DQGDHSLQIG YHHPHAHHHQ AYMDHLSNEA  240
ADMVAHHPNE HIPSGWI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ox0_D4e-25741697101Developmental protein SEPALLATA 3
4ox0_C4e-25741697101Developmental protein SEPALLATA 3
4ox0_B4e-25741697101Developmental protein SEPALLATA 3
4ox0_A4e-25741697101Developmental protein SEPALLATA 3
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.109410.0callus| flower| panicle| root| seed| stem
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasQ10PZ9
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed at early stage of flower development in floral meristem, and at later stage in lemma, palea and carpel primordia. {ECO:0000269|PubMed:11466523}.
UniprotTISSUE SPECIFICITY: Expressed in lemmas, paleas and pistils. Weakly expressed in carpels. {ECO:0000269|PubMed:7948920}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the development of floral organs. Required for the formation of inner floral organs (lodicules, stamens and carpels, or whorls 2, 3 and 4) and the lemma and palea (whorl 1), which are grass floral organs analogous to sepals. May be involved in the control of flowering time. Seems to act as transcriptional activator. May act upstream of the auxin-responsive protein GH3.8. {ECO:0000269|PubMed:10852934, ECO:0000269|PubMed:11466523, ECO:0000269|PubMed:16217607, ECO:0000269|PubMed:7948920, ECO:0000269|Ref.11}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os03g11614.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Interaction ? help Back to Top
Source Intact With
BioGRIDLOC_Os03g54160
IntActSearch Q10PZ9
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Homeotic transformation of lodicules, stamens and carpels into lemma- and palea-like structures. {ECO:0000269|PubMed:10852934}.
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs03g11614
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankFJ7509370.0FJ750937.1 Oryza sativa clone KCS115H08 MADS-box transcription factor 1 mRNA, complete cds.
GenBankAK2890800.0AK289080.1 Oryza sativa Japonica Group cDNA, clone: J090095D11, full insert sequence.
GenBankAK0697280.0AK069728.1 Oryza sativa Japonica Group cDNA clone:J023029M13, full insert sequence.
GenBankRICMADS1TF0.0L34271.1 Oryza sativa box protein (MADS1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015628585.10.0PREDICTED: MADS-box transcription factor 1
SwissprotA2XDY10.0MADS1_ORYSI; MADS-box transcription factor 1
SwissprotQ10PZ90.0MADS1_ORYSJ; MADS-box transcription factor 1
TrEMBLA0A0D3FFG20.0A0A0D3FFG2_9ORYZ; Uncharacterized protein
TrEMBLA0A0D9Z3Y30.0A0A0D9Z3Y3_9ORYZ; Uncharacterized protein
TrEMBLA0A0E0GJ010.0A0A0E0GJ01_ORYNI; Cytochrome b6-f complex subunit 6
TrEMBLA0A0E0NRK30.0A0A0E0NRK3_ORYRU; Uncharacterized protein
TrEMBLD3U2G90.0D3U2G9_ORYSA; MADS-box transcription factor 1
TrEMBLI1P8W50.0I1P8W5_ORYGL; Uncharacterized protein
STRINGLOC_Os03g11614.10.0(Oryza sativa Japonica Group)
STRINGBGIOSGA011213-PA0.0(Oryza sativa Indica Group)
STRINGORGLA03G0081100.10.0(Oryza glaberrima)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP1617761
MonocotsOGMP22213264
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G24260.13e-75MIKC_MADS family protein
Publications ? help Back to Top
  1. Moon YH, et al.
    Determination of the motif responsible for interaction between the rice APETALA1/AGAMOUS-LIKE9 family proteins using a yeast two-hybrid system.
    Plant Physiol., 1999. 120(4): p. 1193-204
    [PMID:10444103]
  2. Jeon JS, et al.
    leafy hull sterile1 is a homeotic mutation in a rice MADS box gene affecting rice flower development.
    Plant Cell, 2000. 12(6): p. 871-84
    [PMID:10852934]
  3. Lim J,Moon YH,An G,Jang SK
    Two rice MADS domain proteins interact with OsMADS1.
    Plant Mol. Biol., 2000. 44(4): p. 513-27
    [PMID:11197326]
  4. Prasad K,Sriram P,Kumar CS,Kushalappa K,Vijayraghavan U
    Ectopic expression of rice OsMADS1 reveals a role in specifying the lemma and palea, grass floral organs analogous to sepals.
    Dev. Genes Evol., 2001. 211(6): p. 281-90
    [PMID:11466523]
  5. Cooper B, et al.
    A network of rice genes associated with stress response and seed development.
    Proc. Natl. Acad. Sci. U.S.A., 2003. 100(8): p. 4945-50
    [PMID:12684538]
  6. Agrawal GK,Abe K,Yamazaki M,Miyao A,Hirochika H
    Conservation of the E-function for floral organ identity in rice revealed by the analysis of tissue culture-induced loss-of-function mutants of the OsMADS1 gene.
    Plant Mol. Biol., 2005. 59(1): p. 125-35
    [PMID:16217607]
  7. Ryu CH, et al.
    OsMADS50 and OsMADS56 function antagonistically in regulating long day (LD)-dependent flowering in rice.
    Plant Cell Environ., 2009. 32(10): p. 1412-27
    [PMID:19558411]
  8. Ren D, et al.
    MULTI-FLORET SPIKELET1, which encodes an AP2/ERF protein, determines spikelet meristem fate and sterile lemma identity in rice.
    Plant Physiol., 2013. 162(2): p. 872-84
    [PMID:23629832]
  9. Chung YY,Kim SR,Finkel D,Yanofsky MF,An G
    Early flowering and reduced apical dominance result from ectopic expression of a rice MADS box gene.
    Plant Mol. Biol., 1994. 26(2): p. 657-65
    [PMID:7948920]