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 Niben101Scf02858g02013.1
Organism
Nicotiana benthamiana
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: 281aa    MW: 31852.9 Da    PI: 7.9908
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Niben101Scf02858g02013.1genomeBTI-
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox581.6e-18118172256
                               T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
                  Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                               rk+ ++tkeq  +Lee F+++++++ +++  LAk+lgL  rqV vWFqNrRa+ k
  Niben101Scf02858g02013.1 118 RKKLRLTKEQSAVLEENFKEHSTLNPKQKLALAKRLGLRARQVEVWFQNRRARTK 172
                               678899***********************************************98 PP
2HD-ZIP_I/II123.31.2e-39118206190
               HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeve 85 
                               +kk+rl+keq+++LEe+F+e+++L+p++K +la++Lgl++rqv+vWFqnrRARtk+kq+E+d+e+Lkr++++l+een+rL+kev+
  Niben101Scf02858g02013.1 118 RKKLRLTKEQSAVLEENFKEHSTLNPKQKLALAKRLGLRARQVEVWFQNRRARTKLKQTEVDCEFLKRCVENLTEENRRLHKEVQ 202
                               69*********************************************************************************** PP

               HD-ZIP_I/II  86 eLree 90 
                               eLr +
  Niben101Scf02858g02013.1 203 ELR-A 206
                               **9.4 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046188.4E-26292IPR006712HD-ZIP protein, N-terminal
SuperFamilySSF466894.28E-18107175IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.604.8E-17109168IPR009057Homeodomain-like
PROSITE profilePS5007117.151114174IPR001356Homeobox domain
SMARTSM003895.4E-15116178IPR001356Homeobox domain
PfamPF000464.3E-16118172IPR001356Homeobox domain
CDDcd000862.85E-14118175No hitNo description
PRINTSPR000313.4E-5145154IPR000047Helix-turn-helix motif
PROSITE patternPS000270149172IPR017970Homeobox, conserved site
PRINTSPR000313.4E-5154170IPR000047Helix-turn-helix motif
Gene3DG3DSA:1.20.5.1709.6E-4169207No hitNo description
SMARTSM003401.1E-25174217IPR003106Leucine zipper, homeobox-associated
PfamPF021832.3E-10174207IPR003106Leucine 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: 281 aa     Download sequence    Send to blast
MEDLGLSLSL SFPENRAVTP VHLNLIRKTS WTDSFPFSDW NSETCGVETR TFLKGIDVNR  60
LPATADAEEE AGVSSPNSTI SSVSGNKRNE REANCEKHDM ERACSRGISD EEDGENCRKK  120
LRLTKEQSAV LEENFKEHST LNPKQKLALA KRLGLRARQV EVWFQNRRAR TKLKQTEVDC  180
EFLKRCVENL TEENRRLHKE VQELRALNLS PQFYMQMTPP TTLTMCPSCE RVASGPTTTP  240
VNLRVGSPQQ QPMPLNLWAT TPNSQGQFGQ IDSYPTLARQ K
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1166174RRARTKLKQ
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}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_019228499.10.0PREDICTED: homeobox-leucine zipper protein HAT4-like isoform X1
SwissprotQ054665e-99HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLA0A314KNB10.0A0A314KNB1_NICAT; Homeobox-leucine zipper protein hat4
STRINGXP_009788263.10.0(Nicotiana sylvestris)
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
AT4G16780.18e-89homeobox 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]