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_Os10g41230.1
Common NameHOX1, LOC4349388, Os10g0561800, OsJ_031189, OSJNBb0089A17.12
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 HD-ZIP
Protein Properties Length: 312aa    MW: 33143.2 Da    PI: 8.9755
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os10g41230.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox59.94.1e-19156210256
                       T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
          Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                       rk+ +++k+q  +Le+ F+++++++ ++++ LA++l+L+ rqV vWFqNrRa+ k
  LOC_Os10g41230.1 156 RKKLRLSKDQAAVLEDTFKEHNTLNPKQKAALARQLNLKPRQVEVWFQNRRARTK 210
                       788899***********************************************98 PP
2HD-ZIP_I/II126.11.5e-40156245191
       HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreel 91 
                       +kk+rlsk+q+++LE++F+e+++L+p++K++lar+L+l+prqv+vWFqnrRARtk+kq+E+d+e Lkr++++l++en+rL++e +eLr +l
  LOC_Os10g41230.1 156 RKKLRLSKDQAAVLEDTFKEHNTLNPKQKAALARQLNLKPRQVEVWFQNRRARTKLKQTEVDCELLKRCCETLTDENRRLHRELQELR-AL 245
                       69*************************************************************************************9.55 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046182.0E-2819135IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.606.0E-19144206IPR009057Homeodomain-like
SuperFamilySSF466899.41E-19147213IPR009057Homeodomain-like
PROSITE profilePS5007117.167152212IPR001356Homeobox domain
SMARTSM003891.0E-16154216IPR001356Homeobox domain
CDDcd000867.84E-16156213No hitNo description
PfamPF000461.7E-16156210IPR001356Homeobox domain
PROSITE patternPS000270187210IPR017970Homeobox, conserved site
SMARTSM003401.0E-23212255IPR003106Leucine zipper, homeobox-associated
PfamPF021834.9E-10212246IPR003106Leucine zipper, homeobox-associated
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
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:0009038anatomypalea
PO:0001048developmental stagepalea development stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 312 aa     Download sequence    Send to blast
MEMMVHGRRD EQYGGLRLGL GLGLSLGVAG GAADDEQPPP RRGAAPPPQQ QLCGWNGGGL  60
FSSSSSDHRG RSAMMACHDV IEMPFLRGID VNRAPAAETT TTTARGPSCS EEDEEPGASS  120
PNSTLSSLSG KRGAPSAATA AAAAASDDED SGGGSRKKLR LSKDQAAVLE DTFKEHNTLN  180
PKQKAALARQ LNLKPRQVEV WFQNRRARTK LKQTEVDCEL LKRCCETLTD ENRRLHRELQ  240
ELRALKLATA AAAPHHLYGA RVPPPTTLTM CPSCERVASA ATTTRNNSGA APARPVPTRP  300
WPPAAAQRSS A*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1154160SRKKLRL
2204212RRARTKLKQ
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.46050.0callus| leaf| panicle| root| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1166331410.0
Expression AtlasQ7XC54-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in root provascular and vascular cylinder, provascular and vascular strands of leaves, provascular and vascular strands of the whole panicle, in mature embryo provascular bundles of scutellum and embryonic axis and provascular and vascular strands of young immature spikelet organs. Expressed in differentiating and differentiated xylem and phloem elements, and in outer and inner bundle sheath cells of all vascular bundles. Expressed in auricles, ligules, culm, guard cells brac hairs and pollen. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:17999151, ECO:0000269|PubMed:9076993}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription repressor involved leaf development. Binds to the DNA sequence 5'-CAAT[GC]ATTG-3'. May act as a regulatory switch to specify provascular cell fate. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:9076993}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os10g41230.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin and sucrose in primary root apical region. By wounding in leaves. {ECO:0000269|PubMed:10732669}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs10g41230
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0654040.0AK065404.1 Oryza sativa Japonica Group cDNA clone:J013006I17, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015613269.10.0homeobox-leucine zipper protein HOX1
SwissprotQ7XC540.0HOX1_ORYSJ; Homeobox-leucine zipper protein HOX1
TrEMBLI1QVY81e-163I1QVY8_ORYGL; Uncharacterized protein
STRINGOS10T0561800-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP25873889
Representative plantOGRP19616156
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G06710.11e-53homeobox from Arabidopsis thaliana
Publications ? help Back to Top
  1. Meijer AH,de Kam RJ,d'Erfurth I,Shen W,Hoge JH
    HD-Zip proteins of families I and II from rice: interactions and functional properties.
    Mol. Gen. Genet., 2000. 263(1): p. 12-21
    [PMID:10732669]
  2. Scarpella E,Boot KJ,Rueb S,Meijer AH
    The procambium specification gene Oshox1 promotes polar auxin transport capacity and reduces its sensitivity toward inhibition.
    Plant Physiol., 2002. 130(3): p. 1349-60
    [PMID:12428000]
  3. Scarpella E,Rueb S,Meijer AH
    The RADICLELESS1 gene is required for vascular pattern formation in rice.
    Development, 2003. 130(4): p. 645-58
    [PMID:12505996]
  4. Rice Chromosome 10 Sequencing Consortium
    In-depth view of structure, activity, and evolution of rice chromosome 10.
    Science, 2003. 300(5625): p. 1566-9
    [PMID:12791992]
  5. 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]
  6. Scarpella E,Simons EJ,Meijer AH
    Multiple regulatory elements contribute to the vascular-specific expression of the rice HD-Zip gene Oshox1 in Arabidopsis.
    Plant Cell Physiol., 2005. 46(8): p. 1400-10
    [PMID:15964905]
  7. Agalou A, et al.
    A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members.
    Plant Mol. Biol., 2008. 66(1-2): p. 87-103
    [PMID:17999151]
  8. Meijer AH, et al.
    Transcriptional repression by Oshox1, a novel homeodomain leucine zipper protein from rice.
    Plant J., 1997. 11(2): p. 263-76
    [PMID:9076993]
  9. Meijer AH,Ouwerkerk PB,Hoge JH
    Vectors for transcription factor cloning and target site identification by means of genetic selection in yeast.
    Yeast, 1998. 14(15): p. 1407-15
    [PMID:9848232]