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 676788896
Organism
Sisymbrium irio
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Sisymbrieae; Sisymbrium
Family HD-ZIP
Protein Properties Length: 289aa    MW: 32078.8 Da    PI: 8.7471
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
676788896genomeVEGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox61.81.1e-19130184256
                T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
   Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                rk+ ++tk+q  +Lee F+ +++++ ++++ LAk+lgL  rqV vWFqNrRa+ k
  676788896 130 RKKLRLTKDQSAILEETFKDHSTLNPKQKQALAKQLGLRARQVEVWFQNRRARTK 184
                78889************************************************98 PP
2HD-ZIP_I/II124.35.8e-40130218190
  HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLree 90 
                  +kk+rl+k+q+++LEe+F+ +++L+p++K++la++Lgl++rqv+vWFqnrRARtk+kq+E+d+e+L+r++++l+een+rL+kev+eLr +
    676788896 130 RKKLRLTKDQSAILEETFKDHSTLNPKQKQALAKQLGLRARQVEVWFQNRRARTKLKQTEVDCEFLRRCCENLTEENRRLQKEVTELR-S 218
                  69*************************************************************************************9.4 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046182.9E-252108IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.604.1E-1899187IPR009057Homeodomain-like
PROSITE profilePS5007117.524126186IPR001356Homeobox domain
SMARTSM003893.4E-16128190IPR001356Homeobox domain
SuperFamilySSF466892.91E-18128195IPR009057Homeodomain-like
PfamPF000463.9E-17130184IPR001356Homeobox domain
CDDcd000862.26E-15130187No hitNo description
PRINTSPR000311.2E-5157166IPR000047Helix-turn-helix motif
PROSITE patternPS000270161184IPR017970Homeobox, conserved site
PRINTSPR000311.2E-5166182IPR000047Helix-turn-helix motif
PfamPF021831.6E-10186219IPR003106Leucine zipper, homeobox-associated
SMARTSM003402.5E-25186229IPR003106Leucine zipper, homeobox-associated
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0008283Biological Processcell proliferation
GO:0009641Biological Processshade avoidance
GO:0009733Biological Processresponse to auxin
GO:0009735Biological Processresponse to cytokinin
GO:0009826Biological Processunidimensional cell growth
GO:0010016Biological Processshoot system morphogenesis
GO:0010017Biological Processred or far-red light signaling pathway
GO:0010218Biological Processresponse to far red light
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048364Biological Processroot development
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0042803Molecular Functionprotein homodimerization activity
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 289 aa     Download sequence    Send to blast
MMLEKDDLGL SLGLNFPNKQ MNLKSNPSAS VAPSSSSFGL LRRSSLNESF NSSVPYSDSS  60
RVETRTLIRG IDVNRPPSTA EYGDEDAGGV SSPNSTVSSS TGKRSEREED TDPQGSRGII  120
SDDEDGDNSR KKLRLTKDQS AILEETFKDH STLNPKQKQA LAKQLGLRAR QVEVWFQNRR  180
ARTKLKQTEV DCEFLRRCCE NLTEENRRLQ KEVTELRSLK LSPQFYMHMS PPTTLTMCPS  240
CEHVSVPPAA PGPQAAASAH HHRSLPVNAW APSTRISHGL TFDALRPRS
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1128134SRKKLRL
2178186RRARTKLKQ
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the negative regulation of cell elongation and specific cell proliferation processes such as lateral root formation and secondary growth of the vascular system. Acts as mediator of the red/far-red light effects on leaf cell expansion in the shading response. Binds to the DNA sequence 5'-CAAT[GC]ATTG-3'. Negatively regulates its own expression. {ECO:0000269|PubMed:10477292, ECO:0000269|PubMed:11260495, ECO:0000269|PubMed:8449400}.
Cis-element ? help Back to Top
SourceLink
PlantRegMap676788896
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Rapidly and strongly induced by lowering the ratio of red to far-red light. {ECO:0000269|PubMed:8106086}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3527050.0AK352705.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-05-E17.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013671709.11e-178homeobox-leucine zipper protein HAT4-like
SwissprotQ054661e-176HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLA0A0D3A7H31e-176A0A0D3A7H3_BRAOL; Uncharacterized protein
STRINGBo1g053220.11e-177(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM15632690
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G16780.11e-158homeobox protein 2
Publications ? help Back to Top
  1. Carabelli M,Turchi L,Ruzza V,Morelli G,Ruberti I
    Homeodomain-Leucine Zipper II family of transcription factors to the limelight: central regulators of plant development.
    Plant Signal Behav, 2014.
    [PMID:23838958]
  2. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  3. Francisco M, et al.
    Genome Wide Association Mapping in Arabidopsis thaliana Identifies Novel Genes Involved in Linking Allyl Glucosinolate to Altered Biomass and Defense.
    Front Plant Sci, 2016. 7: p. 1010
    [PMID:27462337]
  4. Müller-Moulé P, et al.
    YUCCA auxin biosynthetic genes are required for Arabidopsis shade avoidance.
    PeerJ, 2016. 4: p. e2574
    [PMID:27761349]
  5. Ivarson E, et al.
    Effects of Overexpression of WRI1 and Hemoglobin Genes on the Seed Oil Content of Lepidium campestre.
    Front Plant Sci, 2016. 7: p. 2032
    [PMID:28119714]
  6. Kasulin L, et al.
    A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina.
    Mol. Ecol., 2017. 26(13): p. 3389-3404
    [PMID:28316114]
  7. Singh M,Gupta A,Singh D,Khurana JP,Laxmi A
    Arabidopsis RSS1 Mediates Cross-Talk Between Glucose and Light Signaling During Hypocotyl Elongation Growth.
    Sci Rep, 2017. 7(1): p. 16101
    [PMID:29170398]