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_Os03g51690.3
Common NameLOC4333973, Os03g0727000, OSH1, OSJNBa0013A09.5
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 TALE
Protein Properties Length: 243aa    MW: 27632.3 Da    PI: 6.73
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os03g51690.3genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox27.64.9e-091652031755
                       HHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHH CS
          Homeobox  17 elFeknrypsaeereeLAkklgLterqVkvWFqNrRake 55 
                       el +k +yps++++  LA+++gL+ +q+ +WF N+R ++
  LOC_Os03g51690.3 165 ELHYKWPYPSESQKVALAESTGLDLKQINNWFINQRKRH 203
                       5556789*****************************885 PP

2ELK37.84e-13123144122
               ELK   1 ELKhqLlrKYsgyLgsLkqEFs 22 
                       ELKh+Ll+KYsgyL+sLkqE+s
  LOC_Os03g51690.3 123 ELKHHLLKKYSGYLSSLKQELS 144
                       9*******************97 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM012563.7E-283485IPR005541KNOX2
PfamPF037915.8E-234083IPR005541KNOX2
SMARTSM0118818004363IPR005539ELK domain
PROSITE profilePS5121311.331123143IPR005539ELK domain
SMARTSM011884.9E-7123144IPR005539ELK domain
PfamPF037894.9E-10123144IPR005539ELK domain
PROSITE profilePS5007112.617143206IPR001356Homeobox domain
SuperFamilySSF466891.33E-19144219IPR009057Homeodomain-like
SMARTSM003898.5E-13145210IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.606.1E-28148207IPR009057Homeodomain-like
CDDcd000865.04E-12155207No hitNo description
PfamPF059201.7E-16163202IPR008422Homeobox KN domain
PROSITE patternPS000270181204IPR017970Homeobox, 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: 243 aa     Download sequence    Send to blast
MCRGGLQVGA PPEVAARLTA VAQDLELRQR TALGVLGAAT EPELDQFMEA YHEMLVKYRE  60
ELTRPLQEAM EFLRRVETQL NTLSISGRSL RNILSSGSSE EDQEGSGGET ELPEIDAHGV  120
DQELKHHLLK KYSGYLSSLK QELSKKKKKG KLPKDARQQL LNWWELHYKW PYPSESQKVA  180
LAESTGLDLK QINNWFINQR KRHWKPSDEM QFVMMDGYHP TNAAAFYMDG HFINDGGLYR  240
LG*
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 doughnut 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
UniProtProbable transcription factor that regulates genes involved in development. May be involved in shoot formation during embryogenesis. Overexpression in transgenic plants causes altered leaf morphology. Probably binds to the DNA sequence 5'-TGAC-3'. {ECO:0000269|PubMed:10488233, 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_Os03g51690.3
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.
GenBankRICOSH10.0D16507.1 Oryza sativa Japonica Group OSH1 mRNA for homeobox protein, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015629392.11e-174PREDICTED: homeobox protein knotted-1-like 6
SwissprotP466091e-176KNOS6_ORYSJ; Homeobox protein knotted-1-like 6
TrEMBLD6BV171e-174D6BV17_ORYSJ; Homeobox protein
STRINGLOC_Os03g51690.11e-173(Oryza sativa Japonica Group)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G08150.12e-81KNOTTED-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. 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]
  5. 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]
  6. 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]