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 Lus10007849
Organism
Linum usitatissimum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Linaceae; Linum
Family HD-ZIP
Protein Properties Length: 318aa    MW: 34788.8 Da    PI: 9.0487
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Lus10007849genomeBGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox61.61.2e-19157211256
                  T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
     Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                  rk+ +++k+q  +Lee F+++++++ ++++ LAk+lgL  rqV vWFqNrRa+ k
  Lus10007849 157 RKKLRLSKDQSAVLEESFKEHSTLNPKQKQALAKQLGLRPRQVEVWFQNRRARTK 211
                  788899***********************************************98 PP
2HD-ZIP_I/II126.21.5e-40157246191
  HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreel 91 
                  +kk+rlsk+q+++LEesF+e+++L+p++K++la++Lgl+prqv+vWFqnrRARtk+kq+E+d+e+Lkr+ ++l+een+rL+kev+eLr +l
  Lus10007849 157 RKKLRLSKDQSAVLEESFKEHSTLNPKQKQALAKQLGLRPRQVEVWFQNRRARTKLKQTEVDCEFLKRCAENLTEENRRLQKEVQELR-AL 246
                  69*************************************************************************************9.55 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046183.5E-271129IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.606.1E-19143207IPR009057Homeodomain-like
SuperFamilySSF466891.38E-18147214IPR009057Homeodomain-like
PROSITE profilePS5007117.734153213IPR001356Homeobox domain
SMARTSM003893.5E-17155217IPR001356Homeobox domain
PfamPF000464.9E-17157211IPR001356Homeobox domain
CDDcd000862.63E-16157214No hitNo description
PRINTSPR000311.1E-5184193IPR000047Helix-turn-helix motif
PROSITE patternPS000270188211IPR017970Homeobox, conserved site
PRINTSPR000311.1E-5193209IPR000047Helix-turn-helix motif
SMARTSM003404.8E-26213256IPR003106Leucine zipper, homeobox-associated
PfamPF021833.0E-9213247IPR003106Leucine 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: 318 aa     Download sequence    Send to blast
MAEKEGLRLS LSLSFPDHRS PTKTQQLNRL PSVSSSSSAA GKLFAAGANS AALSWLKHHN  60
HNHSALELNP SSDLESERSN SESTRLFLRG IDVNRLPAVP AGVDCDEEAG VSSPNSTVSS  120
ISGKRSERET GGDQDLDGER ASSRGISDEE DGSDTSRKKL RLSKDQSAVL EESFKEHSTL  180
NPKQKQALAK QLGLRPRQVE VWFQNRRART KLKQTEVDCE FLKRCAENLT EENRRLQKEV  240
QELRALKLSP QFYMQMTPPT TLTMCPSCER VAVPPPSSSA STSLPPPVNS TIQHHRPTGV  300
LNPWAAGGAF SALRPRS*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1155161SRKKLRL
2205213RRARTKLKQ
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
PlantRegMapLus10007849
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
GenBankEU8308460.0EU830846.1 Linum usitatissimum clone LU0032D06 mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_021605768.11e-131homeobox-leucine zipper protein HAT4
SwissprotQ054661e-102HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLA0A2C9WC921e-129A0A2C9WC92_MANES; Uncharacterized protein
STRINGLus100078490.0(Linum usitatissimum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF123934105
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G16780.14e-95homeobox 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]