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 XP_016473222.1
Organism
Nicotiana tabacum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana
Family HD-ZIP
Protein Properties Length: 288aa    MW: 32593.6 Da    PI: 8.7007
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_016473222.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox57.71.9e-18136190256
                     T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
        Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                     rk+ +++k+q  +Lee F+++++++ +++  LAk+lgL  rqV vWFqNrRa+ k
  XP_016473222.1 136 RKKLRLSKDQSAVLEETFKEHNTLNPKQKLALAKRLGLRPRQVEVWFQNRRARTK 190
                     788899***********************************************98 PP
2HD-ZIP_I/II128.33.3e-41136225191
     HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreel 91 
                     +kk+rlsk+q+++LEe+F+e+++L+p++K +la++Lgl+prqv+vWFqnrRARtk+kq+E+d+e+Lkr++++l+een+rL+kev+eLr +l
  XP_016473222.1 136 RKKLRLSKDQSAVLEETFKEHNTLNPKQKLALAKRLGLRPRQVEVWFQNRRARTKLKQTEVDCEFLKRCCENLTEENRRLQKEVQELR-AL 225
                     69*************************************************************************************9.55 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046188.0E-334114IPR006712HD-ZIP protein, N-terminal
SuperFamilySSF466894.18E-18129193IPR009057Homeodomain-like
PROSITE profilePS5007117.346132192IPR001356Homeobox domain
SMARTSM003895.9E-16134196IPR001356Homeobox domain
CDDcd000863.93E-15136193No hitNo description
Gene3DG3DSA:1.10.10.601.4E-17136190IPR009057Homeodomain-like
PfamPF000466.1E-16136190IPR001356Homeobox domain
PRINTSPR000312.8E-5163172IPR000047Helix-turn-helix motif
PROSITE patternPS000270167190IPR017970Homeobox, conserved site
PRINTSPR000312.8E-5172188IPR000047Helix-turn-helix motif
PfamPF021832.2E-11192226IPR003106Leucine zipper, homeobox-associated
SMARTSM003404.2E-27192235IPR003106Leucine 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: 288 aa     Download sequence    Send to blast
MKMMVGKEDL GLSLSLSFPD NNNKNSTTNN PLHHQLNLIP SSSPFNLFHK TSWTDSFPSS  60
DRNSEICRVG TRTFLKGIDV NRLPATADAD EEAGVSSPNS TISSVSGNKR SERETNNCEE  120
HEIERASDEE DGETSRKKLR LSKDQSAVLE ETFKEHNTLN PKQKLALAKR LGLRPRQVEV  180
WFQNRRARTK LKQTEVDCEF LKRCCENLTE ENRRLQKEVQ ELRALKLSPQ FYMQMTPPTT  240
LTMCPSCERV AGPPTSSGPT STQVGPTQHR PMPFNLWANT PKSLHPRS
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1134140SRKKLRL
2184192RRARTKLKQ
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}.
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
GenBankAP0107831e-76AP010783.1 Solanum lycopersicum DNA, chromosome 8, clone: C08HBa0006F21, complete sequence.
GenBankHG9755201e-76HG975520.1 Solanum lycopersicum chromosome ch08, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_016473222.10.0PREDICTED: homeobox-leucine zipper protein HAT4-like
SwissprotQ054661e-104HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLA0A1S4A9A00.0A0A1S4A9A0_TOBAC; homeobox-leucine zipper protein HAT4-like
STRINGXP_009589459.10.0(Nicotiana tomentosiformis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA11182485
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G16780.11e-106homeobox 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]