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_Os03g08960.1
Common NameHOX13, LOC4331890, OJ1217B09.11, Os03g0188900
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: 33612.8 Da    PI: 4.4149
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os03g08960.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox59.45.9e-1973125456
                       -SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
          Homeobox   4 RttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                       ++++  eq+++Le+ F  +++++ ++++++A+ lgL+ rqV vWFqNrRa++k
  LOC_Os03g08960.1  73 KRRLALEQVRALERSFDTDNKLDPDRKARIARDLGLQPRQVAVWFQNRRARWK 125
                       4467789*********************************************9 PP
2HD-ZIP_I/II127.84.5e-4171163193
       HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreelke 93 
                       ekkrrl+ eqv++LE+sF++++kL+p+rK+++ar+LglqprqvavWFqnrRAR+ktkqlE+d++aL++++dal+++ ++L++++++L++e++e
  LOC_Os03g08960.1  71 EKKRRLALEQVRALERSFDTDNKLDPDRKARIARDLGLQPRQVAVWFQNRRARWKTKQLERDFAALRARHDALRADCDALRRDKDALAAEIRE 163
                       69**************************************************************************************99986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF466891.21E-1861129IPR009057Homeodomain-like
SMARTSM003894.1E-1970131IPR001356Homeobox domain
PROSITE profilePS5007116.43971127IPR001356Homeobox domain
CDDcd000861.39E-1772128No hitNo description
PfamPF000463.4E-1673125IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.606.7E-2079126IPR009057Homeodomain-like
PRINTSPR000312.8E-598107IPR000047Helix-turn-helix motif
PROSITE patternPS000270102125IPR017970Homeobox, conserved site
PRINTSPR000312.8E-5107123IPR000047Helix-turn-helix motif
PfamPF021832.4E-16127168IPR003106Leucine 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:0020048anatomymicrospore
PO:0001009developmental stageD pollen mother cell meiosis stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 312 aa     Download sequence    Send to blast
MKRPTSSSRK SKKQGEDLAF SEEGSLPAVT MEQKDEAEME EVDEEEEEEV DEDMAGGHAA  60
QSPSPSCGLG EKKRRLALEQ VRALERSFDT DNKLDPDRKA RIARDLGLQP RQVAVWFQNR  120
RARWKTKQLE RDFAALRARH DALRADCDAL RRDKDALAAE IRELREKLPT KPADTAASVK  180
VEAGNDAAAG AAAATVCKDG SSDDSDSSVV FNDEASPYSG AAFIGFGPSF LVDDASAATV  240
GCSSSLPALE SKWHGPYSDD SCKGGVYGFT EEWLAACSGE MAGNDAAGFF SDEHASNLNF  300
GWCASGNEGW E*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1119127RRARWKTKQ
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.380130.0callus| flower| leaf| panicle| root| seed| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329867310.0
Expression AtlasQ10QP3-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in seedlings, roots, stems, leaf sheaths and blades and panicles. {ECO:0000269|PubMed:17999151}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor. {ECO:0000250}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os03g08960.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs03g08960
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1015220.0AK101522.1 Oryza sativa Japonica Group cDNA clone:J033046N04, full insert sequence.
GenBankAK1056440.0AK105644.1 Oryza sativa Japonica Group cDNA clone:001-200-F05, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015628283.10.0homeobox-leucine zipper protein HOX13 isoform X1
SwissprotQ10QP30.0HOX13_ORYSJ; Homeobox-leucine zipper protein HOX13
TrEMBLA0A0E0G2940.0A0A0E0G294_ORYNI; Uncharacterized protein
STRINGOS03T0188900-010.0(Oryza sativa)
STRINGONIVA02G06360.10.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP42833170
Representative plantOGRP1414944
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G40060.13e-28homeobox protein 16
Publications ? help Back to Top
  1. 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]
  2. 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]