PlantTFDB
Plant Transcription Factor Database
v5.0
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Sobic.001G297200.1.p
Common NameSb01g029000, SORBIDRAFT_01g029000
Organism
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; Sorghinae; Sorghum
Family HD-ZIP
Protein Properties Length: 347aa    MW: 37679.1 Da    PI: 8.8256
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.001G297200.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox60.82.2e-19194248256
                           T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
              Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                           rk+ +++k+q  +Le+ F+++++++ ++++ LAk+l+L+ rqV vWFqNrRa+ k
  Sobic.001G297200.1.p 194 RKKLRLSKDQAAVLEDSFKEHNTLNPKQKAALAKQLNLKPRQVEVWFQNRRARTK 248
                           788899***********************************************98 PP

2HD-ZIP_I/II127.65.3e-41194283191
           HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLre 89 
                           +kk+rlsk+q+++LE+sF+e+++L+p++K++la++L+l+prqv+vWFqnrRARtk+kq+E+d+e+Lkr++++l+een+rL++ev+eLr 
  Sobic.001G297200.1.p 194 RKKLRLSKDQAAVLEDSFKEHNTLNPKQKAALAKQLNLKPRQVEVWFQNRRARTKLKQTEVDCEFLKRCCETLTEENRRLQREVAELR- 281
                           69*************************************************************************************9. PP

           HD-ZIP_I/II  90 el 91 
                           +l
  Sobic.001G297200.1.p 282 AL 283
                           55 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046182.8E-2718159IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.601.4E-19179244IPR009057Homeodomain-like
SuperFamilySSF466899.19E-19182251IPR009057Homeodomain-like
PROSITE profilePS5007117.184190250IPR001356Homeobox domain
SMARTSM003892.4E-17192254IPR001356Homeobox domain
PfamPF000461.1E-16194248IPR001356Homeobox domain
CDDcd000861.84E-17194251No hitNo description
PROSITE patternPS000270225248IPR017970Homeobox, conserved site
PfamPF021831.4E-10250284IPR003106Leucine zipper, homeobox-associated
SMARTSM003403.9E-23250293IPR003106Leucine 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
Sequence ? help Back to Top
Protein Sequence    Length: 347 aa     Download sequence    Send to blast
MEMAVNARDE EKKYDGDDNH LGLGLSLSLG IATTAATPVE VDPPPRQQQQ QRAISVAPIS  60
SLPAPQWWNG PAGLFFSPSS GMKMDPSLER KHQHQQQQQQ QAAATSYSHD MPFLRGIDVN  120
RRATAGETRR GRSCSEDEEP GASSPNSTLS SLSGKRAAPA RSSGEVDREA DGHTPRAGGG  180
GSDDEDSGAG GGSRKKLRLS KDQAAVLEDS FKEHNTLNPK QKAALAKQLN LKPRQVEVWF  240
QNRRARTKLK QTEVDCEFLK RCCETLTEEN RRLQREVAEL RALKLVAPHH YARMPPPTTL  300
TMCPSCERLA SAPADEAVAG RTAAPTGPWG PLPVRPVFVD GPARRS*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1192198SRKKLRL
2242250RRARTKLKQ
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Sbi.40240.0callus| embryo
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSobic.001G297200.1.p
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}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEU9424520.0EU942452.1 Zea mays clone 1503625 mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002467488.10.0homeobox-leucine zipper protein HOX1
SwissprotQ406912e-84HOX1_ORYSI; Homeobox-leucine zipper protein HOX1
SwissprotQ7XC542e-84HOX1_ORYSJ; Homeobox-leucine zipper protein HOX1
TrEMBLC5WRJ50.0C5WRJ5_SORBI; Uncharacterized protein
STRINGSb01g029000.10.0(Sorghum bicolor)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP25873889
Representative plantOGRP19616156
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G60390.19e-66homeobox-leucine zipper protein 3
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]