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_Os06g04870.1
Common NameHOX2, LOC4340070, Os06g0140700, OsJ_019261, OsJ_20069, OSJNBa0041F13.48
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: 309aa    MW: 32084.9 Da    PI: 9.1489
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os06g04870.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox60.82.1e-19114168256
                       T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
          Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                       rk+ +++k+q  +Lee+F+ +++++ +++  LA++lgL  rqV vWFqNrRa+ k
  LOC_Os06g04870.1 114 RKKLRLSKDQAAVLEECFKTHSTLNPKQKVALANRLGLRPRQVEVWFQNRRARTK 168
                       678899***********************************************98 PP
2HD-ZIP_I/II124.83.9e-40114204192
       HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreelk 92 
                       +kk+rlsk+q+++LEe+F+++++L+p++Kv+la++Lgl+prqv+vWFqnrRARtk+kq+E+d+e+Lkr++++l++en+rLeke ++Lr +lk
  LOC_Os06g04870.1 114 RKKLRLSKDQAAVLEECFKTHSTLNPKQKVALANRLGLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRWCERLADENKRLEKELADLR-ALK 204
                       69*************************************************************************************9.555 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.605.9E-1898164IPR009057Homeodomain-like
PROSITE profilePS5007116.536110170IPR001356Homeobox domain
SuperFamilySSF466895.01E-18112179IPR009057Homeodomain-like
SMARTSM003891.5E-16112174IPR001356Homeobox domain
PfamPF000469.9E-17114168IPR001356Homeobox domain
CDDcd000865.91E-13114171No hitNo description
PRINTSPR000314.4E-5141150IPR000047Helix-turn-helix motif
PROSITE patternPS000270145168IPR017970Homeobox, conserved site
PRINTSPR000314.4E-5150166IPR000047Helix-turn-helix motif
PfamPF021831.5E-9170204IPR003106Leucine zipper, homeobox-associated
SMARTSM003401.6E-20170213IPR003106Leucine 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: 309 aa     Download sequence    Send to blast
MMDLGLSLGL GLASQGSLTS STTTTSSPGA GSSSPWAAAL NSIVGDVRRD QAAAHAAAAV  60
GVGVGGEEMY QGRASTSPDS AAALSSASGK RERELERSGS GVDDDDGADG AGGRKKLRLS  120
KDQAAVLEEC FKTHSTLNPK QKVALANRLG LRPRQVEVWF QNRRARTKLK QTEVDCEYLK  180
RWCERLADEN KRLEKELADL RALKAAPSPA SASAMQPSSS AAATLTMCPS CRRVATAGAP  240
HQPNHQQCHP KSNTTISSSS TAAAAVAVAG GNVLPSHCQF FPAAAAAADR TSQSTWNAAA  300
PLVTRELF*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1162170RRARTKLKQ
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.23650.0stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO288489390.0
Expression AtlasQ5VPE3-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in seedlings, roots, leaves, nodes, internodes, flowers and embryo. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:17999151}.
UniprotTISSUE SPECIFICITY: Expressed in seedlings, roots, leaves, nodes, internodes, flowers and embryo. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:17999151}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor that binds to the DNA sequence 5'-CAAT[GC]ATTG-3'. {ECO:0000269|PubMed:10732669}.
UniProtProbable transcription factor that binds to the DNA sequence 5'-CAAT[GC]ATTG-3'. {ECO:0000269|PubMed:10732669}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os06g04870.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs06g04870
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1051500.0AK105150.1 Oryza sativa Japonica Group cDNA clone:001-103-D07, full insert sequence.
GenBankAY2068640.0AY206864.1 Oryza sativa (indica cultivar-group) homeodomain leucine zipper protein (Hox2) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015641839.10.0homeobox-leucine zipper protein HOX2
SwissprotQ5VPE30.0HOX2_ORYSJ; Homeobox-leucine zipper protein HOX2
SwissprotQ84U860.0HOX2_ORYSI; Homeobox-leucine zipper protein HOX2
TrEMBLA0A0E0HKR90.0A0A0E0HKR9_ORYNI; Uncharacterized protein
TrEMBLA0A0E0PTA60.0A0A0E0PTA6_ORYRU; Uncharacterized protein
TrEMBLB8B2B60.0B8B2B6_ORYSI; Uncharacterized protein
STRINGORUFI06G02570.10.0(Oryza rufipogon)
STRINGOS06T0140700-010.0(Oryza sativa)
STRINGONIVA06G03250.10.0(Oryza nivara)
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
AT5G06710.15e-51homeobox 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. 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]
  3. 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]