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_Os01g10504.2
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: 277aa    MW: 30902.8 Da    PI: 9.4035
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os01g10504.2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF991.9e-314998150
                      S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE CS
            SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeys 50
                      krien++nrqvtf+kRrng+lKKA+ELSvLCdaeva+i+fss+g+lyey+
  LOC_Os01g10504.2 49 KRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYA 98
                      79***********************************************8 PP
2K-box99.35.6e-33117213499
             K-box   4 ssgks.leeakaeslqqelakLkkeienLq.reqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaL 94 
                       s++   ++e +a+++qqe++kL+++i++Lq  + R ++G++++++sl++L+q+e++Lek++ kiR++Knell++++e++qk+e elq++n++L
  LOC_Os01g10504.2 117 SNS-GtVAEVNAQHYQQESSKLRQQISSLQnANSRTIVGDSINTMSLRDLKQVENRLEKGIAKIRARKNELLYAEVEYMQKREVELQNDNMYL 208
                       333.25999*********************9899*********************************************************** PP

             K-box  95 rkkle 99 
                       r+k+ 
  LOC_Os01g10504.2 209 RSKVV 213
                       **986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004321.1E-4241100IPR002100Transcription factor, MADS-box
PROSITE profilePS5006634.13241101IPR002100Transcription factor, MADS-box
SuperFamilySSF554554.84E-3342113IPR002100Transcription factor, MADS-box
CDDcd002652.72E-4642115No hitNo description
PROSITE patternPS0035004397IPR002100Transcription factor, MADS-box
PRINTSPR004045.9E-334363IPR002100Transcription factor, MADS-box
PfamPF003191.1E-265097IPR002100Transcription factor, MADS-box
PRINTSPR004045.9E-336378IPR002100Transcription factor, MADS-box
PRINTSPR004045.9E-337899IPR002100Transcription factor, MADS-box
PfamPF014861.2E-22126212IPR002487Transcription factor, K-box
PROSITE profilePS5129713.805127218IPR002487Transcription 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:0048366Biological Processleaf development
GO:0048440Biological Processcarpel development
GO:0048497Biological Processmaintenance of floral organ identity
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: 277 aa     Download sequence    Send to blast
MMNMMTDLSC GPSSMTELTA AAAPAGSGSS AAVAAGSSEK MGRGKIEIKR IENTTNRQVT  60
FCKRRNGLLK KAYELSVLCD AEVALIVFSS RGRLYEYANN SVKSTVERYK KANSDTSNSG  120
TVAEVNAQHY QQESSKLRQQ ISSLQNANSR TIVGDSINTM SLRDLKQVEN RLEKGIAKIR  180
ARKNELLYAE VEYMQKREVE LQNDNMYLRS KVVENERGQQ PLNMMGAAST SEYDHMVNNP  240
YDSRNFLQVN IMQQPQHYAH QLQPTTLQLG QQPAFN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A1e-2141128191MEF2C
5f28_B1e-2141128191MEF2C
5f28_C1e-2141128191MEF2C
5f28_D1e-2141128191MEF2C
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed at early stage of flower development in stamen anlagen before stamen initiation, and at later stage in lodicule and ovule primordia initiation region. {ECO:0000269|PubMed:10945340, ECO:0000269|PubMed:16326928}.
UniprotTISSUE SPECIFICITY: Expressed in lemmas, paleas and lodicules. {ECO:0000269|PubMed:10945340}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the development of floral organs. Acts as C-class protein in association with MADS58. Involved in the control of lodicule number (whorl 2), stamen specification (whorl 3) and floral meristem determinacy (whorl 4), but not in the regulation of carpel morphogenesis. Plays a more predominant role in controlling lodicule development and in specifying stamen identity than MADS58. {ECO:0000269|PubMed:11828031, ECO:0000269|PubMed:16326928, ECO:0000269|PubMed:9869408}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00609ChIP-seqTransfer from AT4G18960Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os01g10504.2
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs01g10504
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankRICOSMAB3A0.0L37528.1 Oryza sativa MADS-box protein (MADS3) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015632490.10.0MADS-box transcription factor 3 isoform X1
SwissprotQ407041e-177MADS3_ORYSJ; MADS-box transcription factor 3
TrEMBLA0A0E0FI670.0A0A0E0FI67_ORYNI; Uncharacterized protein
STRINGLPERR01G06160.11e-174(Leersia perrieri)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G18960.11e-102MIKC_MADS family protein
Publications ? help Back to Top
  1. Kyozuka J,Shimamoto K
    Ectopic expression of OsMADS3, a rice ortholog of AGAMOUS, caused a homeotic transformation of lodicules to stamens in transgenic rice plants.
    Plant Cell Physiol., 2002. 43(1): p. 130-5
    [PMID:11828031]
  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]