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 XP_009145468.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family HD-ZIP
Protein Properties Length: 285aa    MW: 31979.8 Da    PI: 9.2766
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009145468.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox611.9e-19128182256
                     T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
        Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                     rk+ +++k+q  +Lee F+ +++++ ++++ LAk+lgL  rqV vWFqNrRa+ k
  XP_009145468.1 128 RKKLRLSKDQSAILEETFKDHSTLNPKQKQALAKQLGLRARQVEVWFQNRRARTK 182
                     788899***********************************************98 PP
2HD-ZIP_I/II124.35.7e-40128216190
     HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLree 90 
                     +kk+rlsk+q+++LEe+F+ +++L+p++K++la++Lgl++rqv+vWFqnrRARtk+kq+E+d+e+L+r++++l+een+rL+kev+eLr +
  XP_009145468.1 128 RKKLRLSKDQSAILEETFKDHSTLNPKQKQALAKQLGLRARQVEVWFQNRRARTKLKQTEVDCEFLRRCCENLTEENRRLQKEVTELR-S 216
                     69*************************************************************************************9.4 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046183.9E-262107IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.604.2E-18115178IPR009057Homeodomain-like
PROSITE profilePS5007117.427124184IPR001356Homeobox domain
SuperFamilySSF466894.28E-18126193IPR009057Homeodomain-like
SMARTSM003895.2E-16126188IPR001356Homeobox domain
CDDcd000865.39E-15128185No hitNo description
PfamPF000467.8E-17128182IPR001356Homeobox domain
PRINTSPR000311.2E-5155164IPR000047Helix-turn-helix motif
PROSITE patternPS000270159182IPR017970Homeobox, conserved site
PRINTSPR000311.2E-5164180IPR000047Helix-turn-helix motif
PfamPF021831.6E-10184217IPR003106Leucine zipper, homeobox-associated
SMARTSM003402.5E-25184227IPR003106Leucine 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: 285 aa     Download sequence    Send to blast
MMFEKDDLGL SLGLNLPKKQ MNLKSNPSVS LTPSSSSFGL LRRSSFNESF NSSVPYSDSS  60
RVETRTFIRG IDVNQPPSTA EYGDKDAGVS SPNSTVSSST GKRSEREEDT DPQGSRGISD  120
DEDGDNSRKK LRLSKDQSAI LEETFKDHST LNPKQKQALA KQLGLRARQV EVWFQNRRAR  180
TKLKQTEVDC EFLRRCCENL TEENRRLQKE VTELRSLKLS PQFYMHMNPP TTLTMCPSCE  240
HVSVPPPPPQ VAASGHHQRS LPVNPWAPAT RVSHGLTFDA FRPRS
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1126132SRKKLRL
2176184RRARTKLKQ
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.105610.0silique
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 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
PlantRegMapXP_009145468.1
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
GenBankAK3527050.0AK352705.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-05-E17.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009145468.10.0PREDICTED: homeobox-leucine zipper protein HAT4
RefseqXP_013733810.10.0homeobox-leucine zipper protein HAT4
SwissprotQ054661e-179HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLA0A3P5ZSU80.0A0A3P5ZSU8_BRACM; Uncharacterized protein
TrEMBLM4FG670.0M4FG67_BRARP; Uncharacterized protein
STRINGBra040094.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM15632690
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G16780.11e-160homeobox 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]