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 Araha.49827s0001.1.p
Organism
Arabidopsis halleri
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family HD-ZIP
Protein Properties Length: 284aa    MW: 31691.4 Da    PI: 8.7507
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Araha.49827s0001.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox59.94e-19127181256
                           T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
              Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                           rk+ +++k+q  +Lee F+ +++++ ++++ LAk+lgL  rqV vWFqNrRa+ k
  Araha.49827s0001.1.p 127 RKKLRLSKDQSVILEETFKDHSTLNPKQKQALAKQLGLRARQVEVWFQNRRARTK 181
                           788899***********************************************98 PP
2HD-ZIP_I/II123.11.3e-39127216191
           HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLre 89 
                           +kk+rlsk+q+ +LEe+F+ +++L+p++K++la++Lgl++rqv+vWFqnrRARtk+kq+E+d+e+L+r++++l+een+rL+kev+eLr 
  Araha.49827s0001.1.p 127 RKKLRLSKDQSVILEETFKDHSTLNPKQKQALAKQLGLRARQVEVWFQNRRARTKLKQTEVDCEFLRRCCENLTEENRRLQKEVTELR- 214
                           69*************************************************************************************9. PP

           HD-ZIP_I/II  90 el 91 
                           +l
  Araha.49827s0001.1.p 215 AL 216
                           55 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046181.7E-272106IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.606.1E-18114177IPR009057Homeodomain-like
PROSITE profilePS5007117.265123183IPR001356Homeobox domain
SuperFamilySSF466895.56E-18125192IPR009057Homeodomain-like
SMARTSM003891.5E-15125187IPR001356Homeobox domain
PfamPF000461.6E-16127181IPR001356Homeobox domain
CDDcd000862.01E-14127184No hitNo description
PRINTSPR000311.1E-5154163IPR000047Helix-turn-helix motif
PROSITE patternPS000270158181IPR017970Homeobox, conserved site
PRINTSPR000311.1E-5163179IPR000047Helix-turn-helix motif
SMARTSM003403.8E-26183226IPR003106Leucine zipper, homeobox-associated
PfamPF021838.3E-11183217IPR003106Leucine 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: 284 aa     Download sequence    Send to blast
MMLEKDDLGL SLGLNFPKKQ INLKTNPSVS VTPSSSSFGL LRRSSWNESF TSSVPNSDSS  60
QKETRTFRGI DVNRPPSTAE YGDEDAGVSS PNSTVSSSTG KRSEREEDTD PQGSRGISDD  120
EDGDNSRKKL RLSKDQSVIL EETFKDHSTL NPKQKQALAK QLGLRARQVE VWFQNRRART  180
KLKQTEVDCE FLRRCCENLT EENRRLQKEV TELRALKLSP QFYMHMSPPT TLTMCPSCEH  240
VSVPPPQPQA ATSADHRSLP VNAWAPATRI SHGLTFDALR PRS*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1125131SRKKLRL
2175183RRARTKLKQ
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
PlantRegMapAraha.49827s0001.1.p
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
GenBankAF3754530.0AF375453.1 Arabidopsis thaliana AT4g16780/dl4415w mRNA, complete cds.
GenBankAY0817470.0AY081747.1 Arabidopsis thaliana AT4g16780/dl4415w mRNA, complete cds.
GenBankX681450.0X68145.1 A.thaliana Athb-2 mRNA.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_193411.10.0homeobox protein 2
SwissprotQ054660.0HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLA0A178V3W80.0A0A178V3W8_ARATH; HB-2
STRINGAT4G16780.10.0(Arabidopsis thaliana)
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
AT4G16780.10.0homeobox 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]