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 mrna08853.1-v1.0-hybrid
Organism
Fragaria vesca
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Rosoideae; Potentilleae; Fragariinae; Fragaria
Family HD-ZIP
Protein Properties Length: 303aa    MW: 34215.5 Da    PI: 8.7256
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
mrna08853.1-v1.0-hybridgenomeGDRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox59.55.5e-19127181256
                              T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
                 Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                              rk+ +++k+q  +Lee F+++++++ +++  LAk+lgL  rqV vWFqNrRa+ k
  mrna08853.1-v1.0-hybrid 127 RKKLRLSKDQSAILEESFKEHNTLNPKQKLALAKQLGLRPRQVEVWFQNRRARTK 181
                              788899***********************************************98 PP
2HD-ZIP_I/II129.61.2e-41127216191
              HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekevee 86 
                              +kk+rlsk+q+++LEesF+e+++L+p++K +la++Lgl+prqv+vWFqnrRARtk+kq+E+d+e+Lkr++++l+een+rL+kev+e
  mrna08853.1-v1.0-hybrid 127 RKKLRLSKDQSAILEESFKEHNTLNPKQKLALAKQLGLRPRQVEVWFQNRRARTKLKQTEVDCEFLKRCCENLTEENRRLQKEVQE 212
                              69************************************************************************************ PP

              HD-ZIP_I/II  87 Lreel 91 
                              Lr +l
  mrna08853.1-v1.0-hybrid 213 LR-AL 216
                              *9.55 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046188.0E-1647101IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.602.9E-18113177IPR009057Homeodomain-like
SuperFamilySSF466891.0E-18117184IPR009057Homeodomain-like
PROSITE profilePS5007117.443123183IPR001356Homeobox domain
SMARTSM003891.2E-16125187IPR001356Homeobox domain
PfamPF000462.0E-16127181IPR001356Homeobox domain
CDDcd000862.38E-15127184No hitNo description
PRINTSPR000312.1E-5154163IPR000047Helix-turn-helix motif
PROSITE patternPS000270158181IPR017970Homeobox, conserved site
PRINTSPR000312.1E-5163179IPR000047Helix-turn-helix motif
SMARTSM003404.2E-27183226IPR003106Leucine zipper, homeobox-associated
PfamPF021832.3E-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:0009734Biological Processauxin-activated signaling pathway
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: 303 aa     Download sequence    Send to blast
MSSNDCDEEG VGKWRDKMTR TTARCGVFVW GPPMWGGRAW ESTCSEGPRR TYRSSDTCRG  60
PARSFLRGID VNRLPSTGDC EDVSSPNSTV SSVSGKRSER EANGEELDLE RDGSRGMSDE  120
EDGETSRKKL RLSKDQSAIL EESFKEHNTL NPKQKLALAK QLGLRPRQVE VWFQNRRART  180
KLKQTEVDCE FLKRCCENLT EENRRLQKEV QELRALKLSP QFYMQMTPPT TLTMCPSCER  240
VAVPPNSTSP SATVDPRAHH HHHHPMVPVH HPRAIPVAGP WAAAAPVLQQ QRQFEPFRTA  300
RP*
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}.
UniProtProbable transcription factor that plays a role in auxin-mediated morphogenesis. Negatively regulates lateral root elongation. {ECO:0000269|PubMed:12492842}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00550DAPTransfer from AT5G47370Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapmrna08853.1-v1.0-hybrid
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By indole-3-acetic acid (IAA). {ECO:0000269|PubMed:12492842}.
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
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004301172.10.0PREDICTED: homeobox-leucine zipper protein HAT4-like
SwissprotP466014e-92HAT2_ARATH; Homeobox-leucine zipper protein HAT2
SwissprotQ054663e-92HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLA0A2P6P8P01e-154A0A2P6P8P0_ROSCH; Putative transcription factor HD-ZIP family
STRINGXP_004301172.10.0(Fragaria vesca)
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
AT4G16780.11e-85homeobox 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. 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]
  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]