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 Brast03G198700.1.p
Organism
Brachypodium stacei
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Pooideae; Brachypodieae; Brachypodium
Family HD-ZIP
Protein Properties Length: 274aa    MW: 28983.8 Da    PI: 10.408
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Brast03G198700.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox603.7e-19125179256
                         T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
            Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                         rk+ +++k+q  +Le+ F+++++++ ++++ LA++lgL  rqV vWFqNrRa+ k
  Brast03G198700.1.p 125 RKKLRLSKDQSAVLEDSFNQHSTLNPKQKAALARQLGLRPRQVEVWFQNRRARTK 179
                         788899***********************************************98 PP
2HD-ZIP_I/II127.94.1e-41125212188
         HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLr 88 
                         +kk+rlsk+q+++LE+sF+++++L+p++K++lar+Lgl+prqv+vWFqnrRARtk+kq+E+d++aL+r++dal+een+rL +ev++L+
  Brast03G198700.1.p 125 RKKLRLSKDQSAVLEDSFNQHSTLNPKQKAALARQLGLRPRQVEVWFQNRRARTKLKQTEVDCDALRRRCDALTEENRRLLREVQALK 212
                         69************************************************************************************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046188.8E-191697IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.602.1E-19110175IPR009057Homeodomain-like
PROSITE profilePS5007117.038121181IPR001356Homeobox domain
SMARTSM003891.7E-17123185IPR001356Homeobox domain
SuperFamilySSF466896.27E-19124190IPR009057Homeodomain-like
PfamPF000461.5E-16125179IPR001356Homeobox domain
CDDcd000862.77E-17125182No hitNo description
PRINTSPR000315.8E-6152161IPR000047Helix-turn-helix motif
PROSITE patternPS000270156179IPR017970Homeobox, conserved site
PRINTSPR000315.8E-6161177IPR000047Helix-turn-helix motif
PfamPF021832.4E-10181212IPR003106Leucine zipper, homeobox-associated
SMARTSM003405.4E-13181223IPR003106Leucine 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: 274 aa     Download sequence    Send to blast
MEMTVVNGGR DHLGLGLGLG LSLGIAGTTS SVEAAAAPQR APTPGQKIRT ASACHEMPLF  60
LRGIDVNRAP AAGHEDEEPG ASSPDSTLST LSGKRGRSAP GAGGREPERG SDDDEDSGSG  120
AGGSRKKLRL SKDQSAVLED SFNQHSTLNP KQKAALARQL GLRPRQVEVW FQNRRARTKL  180
KQTEVDCDAL RRRCDALTEE NRRLLREVQA LKLPLPPPLY VRAPPLTMCP SCERVASSGK  240
PAVVSGNRAA LGSGPWGPGP VRPVFVDRPA QRA*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1123129SRKKLRL
2173181RRARTKLKQ
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
PlantRegMapBrast03G198700.1.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
GenBankAK3669661e-134AK366966.1 Hordeum vulgare subsp. vulgare mRNA for predicted protein, complete cds, clone: NIASHv2049C06.
GenBankAK3685491e-134AK368549.1 Hordeum vulgare subsp. vulgare mRNA for predicted protein, complete cds, clone: NIASHv2075M23.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_003572077.11e-158homeobox-leucine zipper protein HOX1
SwissprotQ406914e-69HOX1_ORYSI; Homeobox-leucine zipper protein HOX1
SwissprotQ7XC544e-69HOX1_ORYSJ; Homeobox-leucine zipper protein HOX1
TrEMBLA0A0Q3JI531e-157A0A0Q3JI53_BRADI; Uncharacterized protein
STRINGBRADI3G33410.11e-156(Brachypodium distachyon)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP25873889
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G17460.12e-52Homeobox-leucine zipper protein 4 (HB-4) / HD-ZIP protein
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]