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 LOC_Os05g34940.2
Common NameLOC4338842, OsJ_18598
Organism
Oryza sativa subsp. japonica
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: 211aa    MW: 24380.8 Da    PI: 9.0978
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os05g34940.2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF85.82.5e-27959151
                      S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
            SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                      krien++nrqvtfskRr+gilKKA E+ vLCdaev v+ifss gkl +y++
  LOC_Os05g34940.2  9 KRIENSTNRQVTFSKRRAGILKKAREIGVLCDAEVGVVIFSSAGKLSDYCT 59
                      79***********************************************96 PP
2K-box67.83.7e-2371167197
             K-box   1 yqkssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenka 93 
                       yq++sgk l+++k++sl+ e++++kke++n+q e+Rh++GedL+sL+ keL  +e++L+++  + R+k +++++++ ++ ++ e+e++    +
  LOC_Os05g34940.2  71 YQTNSGKILWDEKHKSLSAEIDRVKKENDNMQIELRHMKGEDLNSLQPKELIAIEEALNNGQANLRDKMMDHWRMHKRNEKMLEDEHKMLAFR 163
                       89999999************************************************************9988888888888888887777666 PP

             K-box  94 Lrkk 97 
                        +++
  LOC_Os05g34940.2 164 VHQQ 167
                       6665 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004323.5E-39160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006631.469161IPR002100Transcription factor, MADS-box
CDDcd002658.29E-41280No hitNo description
SuperFamilySSF554553.27E-32295IPR002100Transcription factor, MADS-box
PRINTSPR004049.1E-28323IPR002100Transcription factor, MADS-box
PfamPF003192.7E-231057IPR002100Transcription factor, MADS-box
PRINTSPR004049.1E-282338IPR002100Transcription factor, MADS-box
PRINTSPR004049.1E-283859IPR002100Transcription factor, MADS-box
PfamPF014864.8E-1682164IPR002487Transcription factor, K-box
PROSITE profilePS5129712.6984170IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010097Biological Processspecification of stamen identity
GO:0030154Biological Processcell differentiation
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
MGRGKIEIKR IENSTNRQVT FSKRRAGILK KAREIGVLCD AEVGVVIFSS AGKLSDYCTP  60
KTTLSRILEK YQTNSGKILW DEKHKSLSAE IDRVKKENDN MQIELRHMKG EDLNSLQPKE  120
LIAIEEALNN GQANLRDKMM DHWRMHKRNE KMLEDEHKML AFRVHQQEVE LSGGIRELEL  180
GYHHDDRDFA ASMPFTFRVQ PSHPNLQQEK *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tqe_P2e-18171169Myocyte-specific enhancer factor 2B
1tqe_Q2e-18171169Myocyte-specific enhancer factor 2B
1tqe_R2e-18171169Myocyte-specific enhancer factor 2B
1tqe_S2e-18171169Myocyte-specific enhancer factor 2B
6c9l_A2e-18171169Myocyte-specific enhancer factor 2B
6c9l_B2e-18171169Myocyte-specific enhancer factor 2B
6c9l_C2e-18171169Myocyte-specific enhancer factor 2B
6c9l_D2e-18171169Myocyte-specific enhancer factor 2B
6c9l_E2e-18171169Myocyte-specific enhancer factor 2B
6c9l_F2e-18171169Myocyte-specific enhancer factor 2B
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.22140.0panicle
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329854420.0
Expression AtlasB9FPP6-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in lodicules, at intermediate levels in stamens, and weakly in carpels. Expressed in pollen. {ECO:0000269|PubMed:10394955, ECO:0000269|PubMed:12905025, ECO:0000269|Ref.1}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the development of floral organs. B-class protein required for normal development of lodicules and stamens (whorls 2 and 3). May function as a heterodimer with MADS16. {ECO:0000269|PubMed:9869408}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os05g34940.2
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs05g34940
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankRICOSMAA0.0L37527.1 Oryza sativa MADS box protein (MADS4) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015640709.11e-156MADS-box transcription factor 4 isoform X2
SwissprotQ407031e-155MADS4_ORYSJ; MADS-box transcription factor 4
TrEMBLB8AYK11e-155B8AYK1_ORYSI; Uncharacterized protein
TrEMBLB9FPP61e-155B9FPP6_ORYSJ; Uncharacterized protein
STRINGORGLA05G0147400.11e-155(Oryza glaberrima)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G20240.13e-74MIKC_MADS family protein
Publications ? help Back to Top
  1. Ronai Z, et al.
    Transcription factor binding study by capillary zone electrophoretic mobility shift assay.
    Electrophoresis, 2003. 24(1-2): p. 96-100
    [PMID:12652578]
  2. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  3. Kang HG,An G
    Morphological alterations by ectopic expression of the rice OsMADS4 gene in tobacco plants.
    Plant Cell Rep., 2005. 24(2): p. 120-6
    [PMID:15703945]
  4. Cheng CH, et al.
    A fine physical map of the rice chromosome 5.
    Mol. Genet. Genomics, 2005. 274(4): p. 337-45
    [PMID:16261349]
  5. Chen C, et al.
    Adapting rice anther culture to gene transformation and RNA interference.
    Sci. China, C, Life Sci., 2006. 49(5): p. 414-28
    [PMID:17172048]
  6. Yoshida H, et al.
    superwoman1-cleistogamy, a hopeful allele for gene containment in GM rice.
    Plant Biotechnol. J., 2007. 5(6): p. 835-46
    [PMID:17764519]
  7. Yao SG,Ohmori S,Kimizu M,Yoshida H
    Unequal genetic redundancy of rice PISTILLATA orthologs, OsMADS2 and OsMADS4, in lodicule and stamen development.
    Plant Cell Physiol., 2008. 49(5): p. 853-7
    [PMID:18378529]
  8. Seok HY, et al.
    Rice ternary MADS protein complexes containing class B MADS heterodimer.
    Biochem. Biophys. Res. Commun., 2010. 401(4): p. 598-604
    [PMID:20888318]
  9. Wang H, et al.
    OsMADS32 interacts with PI-like proteins and regulates rice flower development.
    J Integr Plant Biol, 2015. 57(5): p. 504-13
    [PMID:25081486]