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 Itr_sc003050.1_g00006.1
Organism
Ipomoea trifida
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea
Family HD-ZIP
Protein Properties Length: 318aa    MW: 35507.3 Da    PI: 9.5897
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Itr_sc003050.1_g00006.1genomeKazusaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox58.11.5e-18139191254
                              T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHH CS
                 Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRak 54 
                              rk+ ++tk+q  +Lee F+++++++ +++  LAk+lgL  rqV vWFqNrRa+
  Itr_sc003050.1_g00006.1 139 RKKLRLTKDQSAILEESFKEHNTLNPKQKLALAKRLGLRPRQVEVWFQNRRAR 191
                              78889***********************************************8 PP
2HD-ZIP_I/II842.2e-27139192154
              HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARt 54 
                              +kk+rl+k+q+++LEesF+e+++L+p++K +la++Lgl+prqv+vWFqnrRAR 
  Itr_sc003050.1_g00006.1 139 RKKLRLTKDQSAILEESFKEHNTLNPKQKLALAKRLGLRPRQVEVWFQNRRARP 192
                              69**************************************************95 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046182.3E-262109IPR006712HD-ZIP protein, N-terminal
SuperFamilySSF466892.87E-17128191IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.607.8E-18130189IPR009057Homeodomain-like
PROSITE profilePS5007116.439135195IPR001356Homeobox domain
SMARTSM003895.7E-15137199IPR001356Homeobox domain
PfamPF000465.4E-16139191IPR001356Homeobox domain
CDDcd000868.51E-15139191No hitNo description
PRINTSPR000313.3E-5166175IPR000047Helix-turn-helix motif
PRINTSPR000313.3E-5175191IPR000047Helix-turn-helix motif
PfamPF021831.4E-11215249IPR003106Leucine zipper, homeobox-associated
SMARTSM003403.7E-26215258IPR003106Leucine 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: 318 aa     Download sequence    Send to blast
MMVGKEDLGL SLSLSFPEMS RNSASATPLP HLNNTFTAHP SPFNLFHKSP WGPESFPSSD  60
RKSETCRTLL KGIDVNRAPA GTDAEEEAGV SSPNSTISSV SGNKRSEREL GMTMNPEEND  120
AERACSRGIS DEEDGETSRK KLRLTKDQSA ILEESFKEHN TLNPKQKLAL AKRLGLRPRQ  180
VEVWFQNRRA RPMLPRILWS SGIKPFPLHG RTKLKQTEVD CEFLKRCYEN LTEENRRLQK  240
EVQELRALKL SPQFYMQMTP PTTLTMCPSC ERVAAPPSAA AASVAPAPAP AQSRPLPFNL  300
WAPHRPFDPA AGRHPRTN
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1137143SRKKLRL
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_019190669.11e-180PREDICTED: homeobox-leucine zipper protein HAT4
SwissprotQ054666e-96HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLA0A1S4A9A01e-136A0A1S4A9A0_TOBAC; homeobox-leucine zipper protein HAT4-like
STRINGXP_009589459.11e-135(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
AT4G16780.16e-91homeobox 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]