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 PGSC0003DMP400045581
Organism
Solanum tuberosum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum
Family HD-ZIP
Protein Properties Length: 276aa    MW: 31223 Da    PI: 8.0477
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PGSC0003DMP400045581genomePGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox58.89.2e-19125179256
                           T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
              Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                           rk+ +++k+q  +Lee F+++++++ +++  LAk+lgL  rqV vWFqNrRa+ k
  PGSC0003DMP400045581 125 RKKLRLSKDQSAILEESFKEHNTLNPKQKLALAKRLGLRPRQVEVWFQNRRARTK 179
                           788899***********************************************98 PP
2HD-ZIP_I/II129.21.7e-41125214191
           HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLre 89 
                           +kk+rlsk+q+++LEesF+e+++L+p++K +la++Lgl+prqv+vWFqnrRARtk+kq+E+d+e+Lkr++++l+een+rL+kev+eLr 
  PGSC0003DMP400045581 125 RKKLRLSKDQSAILEESFKEHNTLNPKQKLALAKRLGLRPRQVEVWFQNRRARTKLKQTEVDCEFLKRCCENLTEENRRLQKEVQELR- 212
                           69*************************************************************************************9. PP

           HD-ZIP_I/II  90 el 91 
                           +l
  PGSC0003DMP400045581 213 AL 214
                           55 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046183.6E-331101IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.602.4E-18104179IPR009057Homeodomain-like
SuperFamilySSF466891.84E-18116182IPR009057Homeodomain-like
PROSITE profilePS5007117.329121181IPR001356Homeobox domain
SMARTSM003893.0E-16123185IPR001356Homeobox domain
PfamPF000463.4E-16125179IPR001356Homeobox domain
CDDcd000862.67E-14125182No hitNo description
PRINTSPR000312.6E-5152161IPR000047Helix-turn-helix motif
PROSITE patternPS000270156179IPR017970Homeobox, conserved site
PRINTSPR000312.6E-5161177IPR000047Helix-turn-helix motif
PfamPF021832.0E-11181215IPR003106Leucine zipper, homeobox-associated
SMARTSM003404.2E-27181224IPR003106Leucine 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: 276 aa     Download sequence    Send to blast
MVEKEDLGLS LSLSFPDNNN KKNTQLNLSP FNLIQKTSWT DSLFPSSDRN IETCRVETRT  60
FLKGIDVNRL PATGEADEEA GVSSPNSTIS SVSGNKRTER EANNCDQEEH EMERGSDEED  120
GETSRKKLRL SKDQSAILEE SFKEHNTLNP KQKLALAKRL GLRPRQVEVW FQNRRARTKL  180
KQTEVDCEFL KRCCENLTEE NRRLQKEVQE LRALKLSPQF YMQMTPPTTL TMCPSCERVA  240
GPPSSSSGPT STPMGQAQPR PRPFNLWANA LHPRS*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1123129SRKKLRL
2173181RRARTKLKQ
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
PlantRegMapPGSC0003DMP400045581
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
GenBankHG9754471e-154HG975447.1 Solanum pennellii chromosome ch08, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006359253.10.0PREDICTED: homeobox-leucine zipper protein HAT4
SwissprotQ054661e-103HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLM1CHH00.0M1CHH0_SOLTU; Uncharacterized protein
STRINGPGSC0003DMT4000675400.0(Solanum tuberosum)
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-101homeobox protein 2
Publications ? help Back to Top
  1. Xu X, et al.
    Genome sequence and analysis of the tuber crop potato.
    Nature, 2011. 475(7355): p. 189-95
    [PMID:21743474]
  2. 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]
  3. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  4. 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]
  5. Müller-Moulé P, et al.
    YUCCA auxin biosynthetic genes are required for Arabidopsis shade avoidance.
    PeerJ, 2016. 4: p. e2574
    [PMID:27761349]
  6. 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]
  7. 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]
  8. 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]