PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Solyc06g060830.2.1
Common NameLOC101249931
Organism
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; Lycopersicon
Family HD-ZIP
Protein Properties Length: 299aa    MW: 33906.1 Da    PI: 8.1559
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc06g060830.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox59.84.5e-19128182256
                         T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
            Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                         rk+ ++tkeq  +Le+ F+ +++++ +++  LAk+lgL  rqV vWFqNrRa+ k
  Solyc06g060830.2.1 128 RKKLRLTKEQSAVLEDSFKDHHTLNPKQKLALAKRLGLRPRQVEVWFQNRRARTK 182
                         678899***********************************************98 PP

2HD-ZIP_I/II126.89.5e-41128217191
         HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreel 91 
                         +kk+rl+keq+++LE+sF+ +++L+p++K +la++Lgl+prqv+vWFqnrRARtk+kq+E+d+e+Lkr++++l++en+rL+kev+eLr +l
  Solyc06g060830.2.1 128 RKKLRLTKEQSAVLEDSFKDHHTLNPKQKLALAKRLGLRPRQVEVWFQNRRARTKLKQTEVDCEFLKRCVENLTDENRRLQKEVQELR-SL 217
                         69*************************************************************************************9.55 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046183.6E-302101IPR006712HD-ZIP protein, N-terminal
SuperFamilySSF466891.0E-18119185IPR009057Homeodomain-like
PROSITE profilePS5007117.022124184IPR001356Homeobox domain
SMARTSM003891.1E-17126188IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.603.0E-18128180IPR009057Homeodomain-like
CDDcd000864.13E-16128185No hitNo description
PfamPF000462.0E-16128182IPR001356Homeobox domain
PRINTSPR000313.0E-5155164IPR000047Helix-turn-helix motif
PROSITE patternPS000270159182IPR017970Homeobox, conserved site
PRINTSPR000313.0E-5164180IPR000047Helix-turn-helix motif
CDDcd146860.00943177216No hitNo description
Gene3DG3DSA:1.20.5.1708.2E-4181217No hitNo description
PfamPF021834.3E-10184218IPR003106Leucine zipper, homeobox-associated
SMARTSM003402.3E-25184227IPR003106Leucine zipper, homeobox-associated
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 299 aa     Download sequence    Send to blast
MMMEKEDLGL SLSLNFPAEK RTTTTNLISL PPSSSFNNNY WTTHPPFPHS SSDRNMETRS  60
FLKGIDVNRM PAMAAEEEEG GVSSPNSTIS SLSGNKRSER EGNCTEENEM ERASSRGISD  120
EEDGETCRKK LRLTKEQSAV LEDSFKDHHT LNPKQKLALA KRLGLRPRQV EVWFQNRRAR  180
TKLKQTEVDC EFLKRCVENL TDENRRLQKE VQELRSLKHS PQFYMQMTPP TTLTMCPSCE  240
RVATGPTNTP VSIPPHRVGP PHQHHQPMPL NMWDSSSTPI SQGHYGQVDT YPSLARQK*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1176184RRARTKLKQ
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Les.164120.0floral bud| fruit| leaf| seed
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Predominantly expressed in leaves and stems. {ECO:0000269|PubMed:8106086}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor. {ECO:0000250}.
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
PlantRegMapSolyc06g060830.2.1
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
GenBankAP0107838e-61Solanum lycopersicum DNA, chromosome 8, clone: C08HBa0006F21, complete sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004241991.10.0homeobox-leucine zipper protein HAT4
SwissprotP466004e-95HAT1_ARATH; Homeobox-leucine zipper protein HAT1
SwissprotQ054664e-95HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLA0A3Q7GV470.0A0A3Q7GV47_SOLLC; Uncharacterized protein
STRINGSolyc06g060830.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA11182485
Representative plantOGRP19616156
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G16780.11e-95homeobox protein 2
Publications ? help Back to Top
  1. Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD
    Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
    Theor. Appl. Genet., 2005. 112(1): p. 72-84
    [PMID:16208505]
  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. Zou LJ, et al.
    Role of Transcription Factor HAT1 in Modulating Arabidopsis thaliana Response to Cucumber mosaic virus.
    Plant Cell Physiol., 2016. 57(9): p. 1879-89
    [PMID:27328697]
  5. Lozano-Sotomayor P, et al.
    Altered expression of the bZIP transcription factor DRINK ME affects growth and reproductive development in Arabidopsis thaliana.
    Plant J., 2016. 88(3): p. 437-451
    [PMID:27402171]
  6. 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]
  7. Müller-Moulé P, et al.
    YUCCA auxin biosynthetic genes are required for Arabidopsis shade avoidance.
    PeerJ, 2016. 4: p. e2574
    [PMID:27761349]
  8. 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]
  9. 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]
  10. 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]
  11. Tan W, et al.
    Transcription factor HAT1 is a substrate of SnRK2.3 kinase and negatively regulates ABA synthesis and signaling in Arabidopsis responding to drought.
    PLoS Genet., 2018. 14(4): p. e1007336
    [PMID:29659577]