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_Os06g04850.1
Common NameHOX28, LOC4340069, Os06g0140400, OsJ_019259, OSJNBa0041F13.45
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: 257aa    MW: 27016.7 Da    PI: 9.0308
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os06g04850.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox61.81.1e-1993147256
                       T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
          Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                       rk+ +++k+q  +Lee+F+ +++++ +++  LAk+l+L  rqV vWFqNrRa+ k
  LOC_Os06g04850.1  93 RKKLRLSKDQAAVLEECFKTHHTLTPKQKVALAKSLNLRPRQVEVWFQNRRARTK 147
                       788899***********************************************98 PP
2HD-ZIP_I/II125.23e-4093183192
       HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreelk 92 
                       +kk+rlsk+q+++LEe+F+++++L+p++Kv+la++L+l+prqv+vWFqnrRARtk+kq+E+d+e+Lkr++d+l+++n+rL+ke +eLr +lk
  LOC_Os06g04850.1  93 RKKLRLSKDQAAVLEECFKTHHTLTPKQKVALAKSLNLRPRQVEVWFQNRRARTKLKQTEVDCEHLKRWCDQLADDNRRLHKELAELR-ALK 183
                       69*************************************************************************************9.555 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.601.2E-1874147IPR009057Homeodomain-like
SuperFamilySSF466894.71E-1978150IPR009057Homeodomain-like
PROSITE profilePS5007116.66589149IPR001356Homeobox domain
SMARTSM003892.8E-1791153IPR001356Homeobox domain
CDDcd000864.22E-1693150No hitNo description
PfamPF000466.8E-1793147IPR001356Homeobox domain
PROSITE patternPS000270124147IPR017970Homeobox, conserved site
PfamPF021835.0E-11149183IPR003106Leucine zipper, homeobox-associated
SMARTSM003401.3E-19149192IPR003106Leucine 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:0009047anatomystem
PO:0007010developmental stagewhole plant fruit ripening stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 257 aa     Download sequence    Send to blast
MERQGLDLGL SLGLGLTTAA TWPAAGFCLN SGMAEQEVIR RDDVVAATAA EDERFACSPG  60
SPVSSGSGKR GSGSGSGDEV DDAGCDVGGG GARKKLRLSK DQAAVLEECF KTHHTLTPKQ  120
KVALAKSLNL RPRQVEVWFQ NRRARTKLKQ TEVDCEHLKR WCDQLADDNR RLHKELAELR  180
ALKATPTPPA AAPPLTTLTM CLSCKRVANA GVPSPAAAIF PGHPQFLCGF RDHAGAASSS  240
YGGASSGLAK AVRAAR*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1141149RRARTKLKQ
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.376180.0callus| leaf| panicle| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1172404100.0
Expression AtlasQ5VPE5-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in seedlings, roots, stems and panicles. {ECO:0000269|PubMed:17999151}.
UniprotTISSUE SPECIFICITY: Expressed in seedlings, roots, stems and panicles. {ECO:0000269|PubMed:17999151}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor. {ECO:0000250}.
UniProtProbable transcription factor. {ECO:0000250}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os06g04850.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs06g04850
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0591160.0AK059116.1 Oryza sativa Japonica Group cDNA clone:001-022-E09, full insert sequence.
GenBankEU8475160.0EU847516.1 Oryza sativa Japonica Group clone OsHD2B homeobox leucine zipper protein mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015642539.10.0homeobox-leucine zipper protein HOX28
SwissprotA2Y9310.0HOX28_ORYSI; Homeobox-leucine zipper protein HOX28
SwissprotQ5VPE50.0HOX28_ORYSJ; Homeobox-leucine zipper protein HOX28
TrEMBLA0A0E0PTA40.0A0A0E0PTA4_ORYRU; Uncharacterized protein
TrEMBLB7E3F10.0B7E3F1_ORYSJ; Homeobox leucine zipper protein
STRINGORUFI06G02550.10.0(Oryza rufipogon)
STRINGOS06T0140400-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP38423376
Representative plantOGRP19616156
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G06710.11e-45homeobox from Arabidopsis thaliana
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]