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_Os09g29460.1
Common NameHOX4, LOC4347333, OJ1595_D08.21, Os09g0470500
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 HD-ZIP
Protein Properties Length: 278aa    MW: 29392.3 Da    PI: 4.3585
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os09g29460.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox59.45.9e-1951104356
                       --SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
          Homeobox   3 kRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                       k+++++ eq+++Le+ Fe ++++  e++++LA+ lgL+ rqV vWFqNrRa++k
  LOC_Os09g29460.1  51 KKRRLSVEQVRALERSFEVENKLEPERKARLARDLGLQPRQVAVWFQNRRARWK 104
                       456899***********************************************9 PP

2HD-ZIP_I/II132.81.3e-4250142193
       HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreelke 93 
                       ekkrrls eqv++LE+sFe e+kLeperK++lar+LglqprqvavWFqnrRAR+ktkqlE+dy+aL+++yd+l+ ++++L++++++L +e+ke
  LOC_Os09g29460.1  50 EKKRRLSVEQVRALERSFEVENKLEPERKARLARDLGLQPRQVAVWFQNRRARWKTKQLERDYAALRHSYDSLRLDHDALRRDKDALLAEIKE 142
                       69**************************************************************************************99987 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF466891.3E-1939108IPR009057Homeodomain-like
PROSITE profilePS5007117.29746106IPR001356Homeobox domain
SMARTSM003892.1E-1849110IPR001356Homeobox domain
CDDcd000866.57E-1851107No hitNo description
PfamPF000463.0E-1651104IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.601.3E-1953113IPR009057Homeodomain-like
PRINTSPR000319.5E-67786IPR000047Helix-turn-helix motif
PROSITE patternPS00027081104IPR017970Homeobox, conserved site
PRINTSPR000319.5E-686102IPR000047Helix-turn-helix motif
PfamPF021835.4E-17106147IPR003106Leucine 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:0009037anatomylemma
PO:0001047developmental stagelemma development stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 278 aa     Download sequence    Send to blast
MKRPGGAGGG GGSPSLVTMA NSSDDGYGGV GMEAEGDVEE EMMACGGGGE KKRRLSVEQV  60
RALERSFEVE NKLEPERKAR LARDLGLQPR QVAVWFQNRR ARWKTKQLER DYAALRHSYD  120
SLRLDHDALR RDKDALLAEI KELKAKLGDE EAAASFTSVK EEPAASDGPP AAGFGSSDSD  180
SSAVLNDVDA AGAAPAATDA LAPEACTFLG APPAAGAGAG AAAAASHEEV FFHGNFLKVE  240
EDETGFLDDD EPCGGFFADD QPPPLSSWWA EPTEHWN*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
17581ERKARLA
298106RRARWKTKQ
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.23640.0flower| leaf| panicle| root| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329906930.0
Expression AtlasQ6K498-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in leaf and floral organ primordia, floral meristems, embryonic axis and cells surrounding the vascular bundles. Expressed in the vasculature of roots, stem, leaves and spikelets, and in the vascular bundle of the scutellum in embryos. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:17999151, ECO:0000269|PubMed:18049796}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription activator that binds to the DNA sequence 5'-CAAT[AT]ATTG-3'. May be involved in the regulation of gibberellin signaling. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:18049796}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os09g29460.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By gibberellin. Down-regulated in leaves by drought stress. {ECO:0000269|PubMed:17999151, ECO:0000269|PubMed:18049796}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs09g29460
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1054840.0AK105484.1 Oryza sativa Japonica Group cDNA clone:001-127-B05, full insert sequence.
GenBankAK0997100.0AK099710.1 Oryza sativa Japonica Group cDNA clone:J013077J22, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015612509.10.0PREDICTED: homeobox-leucine zipper protein HOX4
SwissprotQ6K4980.0HOX4_ORYSJ; Homeobox-leucine zipper protein HOX4
SwissprotQ9XH370.0HOX4_ORYSI; Homeobox-leucine zipper protein HOX4
TrEMBLA0A0E0IL300.0A0A0E0IL30_ORYNI; Uncharacterized protein
TrEMBLA0A0E0QSM30.0A0A0E0QSM3_ORYRU; Uncharacterized protein
TrEMBLB8BCN80.0B8BCN8_ORYSI; Putative uncharacterized protein
STRINGBGIOSGA030941-PA0.0(Oryza sativa Indica Group)
STRINGLOC_Os09g29460.10.0(Oryza sativa Japonica Group)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP12916189
MonocotsOGMP30093482
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G40060.13e-39homeobox protein 16
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. 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]
  3. Dai M,Hu Y,Ma Q,Zhao Y,Zhou DX
    Functional analysis of rice HOMEOBOX4 (Oshox4) gene reveals a negative function in gibberellin responses.
    Plant Mol. Biol., 2008. 66(3): p. 289-301
    [PMID:18049796]