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_Os03g51690.2
Common NameLOC4333973, Os03g0727000, OSH1, OSJNBa0013A09.5
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 TALE
Protein Properties Length: 362aa    MW: 39898 Da    PI: 6.8667
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os03g51690.2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox26.98e-092843221755
                       HHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHH CS
          Homeobox  17 elFeknrypsaeereeLAkklgLterqVkvWFqNrRake 55 
                       el +k +yps++++  LA+++gL+ +q+ +WF N+R ++
  LOC_Os03g51690.2 284 ELHYKWPYPSESQKVALAESTGLDLKQINNWFINQRKRH 322
                       5566789*****************************885 PP
2ELK37.16.7e-13242263122
               ELK   1 ELKhqLlrKYsgyLgsLkqEFs 22 
                       ELKh+Ll+KYsgyL+sLkqE+s
  LOC_Os03g51690.2 242 ELKHHLLKKYSGYLSSLKQELS 263
                       9*******************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM012552.1E-22102146IPR005540KNOX1
PfamPF037902.2E-23103144IPR005540KNOX1
SMARTSM012563.7E-28153204IPR005541KNOX2
PfamPF037911.1E-22159202IPR005541KNOX2
SMARTSM011881800162182IPR005539ELK domain
PROSITE profilePS5121311.331242262IPR005539ELK domain
PfamPF037898.2E-10242263IPR005539ELK domain
SMARTSM011884.9E-7242263IPR005539ELK domain
PROSITE profilePS5007112.617262325IPR001356Homeobox domain
SuperFamilySSF466892.82E-19263338IPR009057Homeodomain-like
SMARTSM003898.5E-13264329IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.601.2E-27267326IPR009057Homeodomain-like
CDDcd000861.29E-12274326No hitNo description
PfamPF059203.0E-16282321IPR008422Homeobox KN domain
PROSITE patternPS000270300323IPR017970Homeobox, conserved site
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0001708Biological Processcell fate specification
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010051Biological Processxylem and phloem pattern formation
GO:0010089Biological Processxylem development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0043565Molecular Functionsequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009049anatomyinflorescence
PO:0001083developmental stageinflorescence development stage
PO:0007006developmental stageIL.00 inflorescence just visible stage
Sequence ? help Back to Top
Protein Sequence    Length: 362 aa     Download sequence    Send to blast
MEEISHHFGV VGASGVHGGH QHQHHHHPWG SSLSAIVAPP PPPQLQQQQT QAGGMAHTPL  60
TLNTAAAAVG NPVLQLANGS LLDACGKAKE ASASASYAAD VEAIKAKIIS HPHYSSLLAA  120
YLDCQKVGAP PEVAARLTAV AQDLELRQRT ALGVLGAATE PELDQFMEAY HEMLVKYREE  180
LTRPLQEAME FLRRVETQLN TLSISGRSLR NILSSGSSEE DQEGSGGETE LPEIDAHGVD  240
QELKHHLLKK YSGYLSSLKQ ELSKKKKKGK LPKDARQQLL NWWELHYKWP YPSESQKVAL  300
AESTGLDLKQ INNWFINQRK RHWKPSDEMQ FVMMDGYHPT NAAAFYMDGH FINDGGLYRL  360
G*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.1510.0panicle| root| stem| vegetative meristem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO4522350.0
Expression AtlasP46609-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in the globular stage embryo 2 days after pollination (DAP) in a restricted small region just below the center of the ventral region of the embryo, where the shoot apex arises later. From 3 to 4 DAP expressed in an enlarged ventral region of embryo, corresponding to the expected epiblast and radicle, respectively. At the shoot apex differentiation stage (4-5 DAP), expressed in the shoot apex, epiblast, radicle primordia, and in their intervening tissues. Expression in the radicle is observed in the cells surrounding the root apical meristem in a donut shape but not in the meristem. During the first and second leaf primordium formation, expression pattern is maintained, but decreases. During inflorescence development, expressed only in the corpus of the rachis primordium but not in the tunica layer (L1). After floral induction, expressed in both tunica and corpus but not in floral organ primordia. Later in flower development, expressed in the corpus of the floral meristem. {ECO:0000269|PubMed:10488233, ECO:0000269|PubMed:8755613, ECO:0000269|PubMed:9869405}.
UniprotTISSUE SPECIFICITY: Expressed predominantly in shoot apices. Also found to a lesser extent in glumes.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that regulates genes involved in development. May be involved in shoot formation during embryogenesis. Overexpression in transgenic plants causes altered leaf morphology (PubMed:10488233, PubMed:8755613, PubMed:9869405). Regulates anther dehiscence via direct repression of the auxin biosynthetic gene YUCCA4 (PubMed:29915329). Binds to the DNA sequence 5'-TGAC-3' in the promoter of the YUCCA4 gene and represses its activity during anther development (PubMed:29915329). Reduction of auxin levels at late stage of anther development, after meiosis of microspore mother cells, is necessary for normal anther dehiscence and seed setting (PubMed:29915329). {ECO:0000269|PubMed:10488233, ECO:0000269|PubMed:29915329, ECO:0000269|PubMed:8755613, ECO:0000269|PubMed:9869405}.
Function -- GeneRIF ? help Back to Top
  1. Positive autoregulation of OSH1 is essential for its expression and shoot apical meristem maintenance.
    [PMID: 22207572]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00675ChIP-seqTransfer from GRMZM2G017087Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os03g51690.2
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs03g51690
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankFJ9402060.0FJ940206.1 Oryza sativa Japonica Group clone KCB522D03 homeobox protein mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015629392.10.0homeobox protein knotted-1-like 6
SwissprotP466090.0KNOS6_ORYSJ; Homeobox protein knotted-1-like 6
TrEMBLD6BV170.0D6BV17_ORYSJ; Homeobox protein
STRINGORGLA03G0296100.10.0(Oryza glaberrima)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G08150.11e-96KNOTTED-like from Arabidopsis thaliana
Publications ? help Back to Top
  1. Sentoku N, et al.
    Regional expression of the rice KN1-type homeobox gene family during embryo, shoot, and flower development.
    Plant Cell, 1999. 11(9): p. 1651-64
    [PMID:10488233]
  2. Jain M,Tyagi AK,Khurana JP
    Genome-wide identification, classification, evolutionary expansion and expression analyses of homeobox genes in rice.
    FEBS J., 2008. 275(11): p. 2845-61
    [PMID:18430022]
  3. Tsuda K,Ito Y,Sato Y,Kurata N
    Positive autoregulation of a KNOX gene is essential for shoot apical meristem maintenance in rice.
    Plant Cell, 2011. 23(12): p. 4368-81
    [PMID:22207572]
  4. Song S, et al.
    OsFTIP7 determines auxin-mediated anther dehiscence in rice.
    Nat Plants, 2018. 4(7): p. 495-504
    [PMID:29915329]
  5. Matsuoka M, et al.
    Expression of a rice homeobox gene causes altered morphology of transgenic plants.
    Plant Cell, 1993. 5(9): p. 1039-48
    [PMID:8104574]
  6. Sato Y, et al.
    A rice homeobox gene, OSH1, is expressed before organ differentiation in a specific region during early embryogenesis.
    Proc. Natl. Acad. Sci. U.S.A., 1996. 93(15): p. 8117-22
    [PMID:8755613]
  7. Sato Y,Sentoku N,Nagato Y,Matsuoka M
    Isolation and characterization of a rice homebox gene, OSH15.
    Plant Mol. Biol., 1998. 38(6): p. 983-98
    [PMID:9869405]