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 Sof007970
Organism
Saccharum officinarum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Saccharinae; Saccharum; Saccharum officinarum complex
Family HD-ZIP
Protein Properties Length: 304aa    MW: 32859.3 Da    PI: 9.3066
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PUT-157a-Saccharum_officinarum-95677PU_refplantGDBView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox61.11.8e-19191245256
                T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
   Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                rk+ +++k+q  +Le+ F+++++++ ++++ LAk+l+L+ rqV vWFqNrRa+ k
  Sof007970 191 RKKLRLSKDQAAVLEDSFKEHNTLNPKQKAALAKQLNLKPRQVEVWFQNRRARTK 245
                788899***********************************************98 PP
2HD-ZIP_I/II113.11.8e-36191267177
  HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeen 77 
                  +kk+rlsk+q+++LE+sF+e+++L+p++K++la++L+l+prqv+vWFqnrRARtk+kq+E+d+e+Lkr +++l e++
    Sof007970 191 RKKLRLSKDQAAVLEDSFKEHNTLNPKQKAALAKQLNLKPRQVEVWFQNRRARTKLKQTEVDCEFLKRFCKTLPEKT 267
                  69********************************************************************9998765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046181.9E-2315157IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.601.1E-19176241IPR009057Homeodomain-like
SuperFamilySSF466896.84E-19179248IPR009057Homeodomain-like
PROSITE profilePS5007117.184187247IPR001356Homeobox domain
SMARTSM003892.4E-17189251IPR001356Homeobox domain
CDDcd000861.03E-17191248No hitNo description
PfamPF000468.8E-17191245IPR001356Homeobox domain
PROSITE patternPS000270222245IPR017970Homeobox, conserved site
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 304 aa     Download sequence    Send to blast
MEMAVNARDE EQYGKNDNHL GLGLSLSLGI ATAAPVEVEP PPAPPRQQQQ QRAISVEPIS  60
SLLPAPQWWN GPAGLFFSPS SGMMDPSLER KHQHQPQPPS TCHSHEMPFL RLRGIDVNRA  120
PAAGETGRRG SCSEDEEPGA SSPNSTLSSL SGKRAAPARS SGEVDREADH TPRAGGGGSD  180
DEDSGAGGGS RKKLRLSKDQ AAVLEDSFKE HNTLNPKQKA ALAKQLNLKP RQVEVWFQNR  240
RARTKLKQTE VDCEFLKRFC KTLPEKTRGC NGSWGLPXLK LVGADHYGRI GGGTKLNMGP  300
SGRX
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1189195SRKKLRL
2239247RRARTKLKQ
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Sof.133640.0bud| callus| crown| stem
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}.
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:10934011, 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:10934011, ECO:0000269|PubMed:9076993}.
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}.
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}.
UniProtINDUCTION: By auxin and sucrose in primary root apical region. By wounding in leaves. {ECO:0000269|PubMed:10934011}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002467488.11e-135homeobox-leucine zipper protein HOX1
SwissprotQ406911e-57HOX1_ORYSI; Homeobox-leucine zipper protein HOX1
SwissprotQ7XC541e-57HOX1_ORYSJ; Homeobox-leucine zipper protein HOX1
TrEMBLC5WRJ51e-133C5WRJ5_SORBI; Uncharacterized protein
STRINGSb01g029000.11e-134(Sorghum bicolor)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G16780.12e-42homeobox protein 2
Publications ? help Back to Top
  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]