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 Cagra.0812s0021.1.p
Organism
Capsella grandiflora
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family HD-ZIP
Protein Properties Length: 290aa    MW: 32215.9 Da    PI: 8.7434
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.0812s0021.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox60.92e-19129183256
                          T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
             Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                          rk+ +++k+q  +Lee F+ +++++ ++++ LAk+lgL  rqV vWFqNrRa+ k
  Cagra.0812s0021.1.p 129 RKKLRLSKDQSAILEETFKDHSTLNPKQKQALAKQLGLRARQVEVWFQNRRARTK 183
                          788899***********************************************98 PP
2HD-ZIP_I/II124.35.7e-40129218191
          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 +
  Cagra.0812s0021.1.p 129 RKKLRLSKDQSAILEETFKDHSTLNPKQKQALAKQLGLRARQVEVWFQNRRARTKLKQTEVDCEFLRRCCENLTEENRRLQKEVTELR-A 217
                          69*************************************************************************************9.5 PP

          HD-ZIP_I/II  91 l 91 
                          l
  Cagra.0812s0021.1.p 218 L 218
                          5 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046188.4E-282107IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.602.9E-1898186IPR009057Homeodomain-like
PROSITE profilePS5007117.427125185IPR001356Homeobox domain
SMARTSM003895.2E-16127189IPR001356Homeobox domain
SuperFamilySSF466894.71E-18127194IPR009057Homeodomain-like
PfamPF000467.9E-17129183IPR001356Homeobox domain
CDDcd000867.08E-15129186No hitNo description
PRINTSPR000311.2E-5156165IPR000047Helix-turn-helix motif
PROSITE patternPS000270160183IPR017970Homeobox, conserved site
PRINTSPR000311.2E-5165181IPR000047Helix-turn-helix motif
PfamPF021838.5E-11185219IPR003106Leucine zipper, homeobox-associated
SMARTSM003403.8E-26185228IPR003106Leucine 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: 290 aa     Download sequence    Send to blast
MMLEKDDLGL SLGLNYPKKQ MNLNSNPSVS VTPSSSSFGL LRRSSLNESF TSSVPNSDSS  60
QKETRTFIRG IDVNRPPSTA EYGEEEAGVS SPNSTVSSST GKRSEREEDT DPQGSRGGIS  120
DDEDGDNSRK KLRLSKDQSA ILEETFKDHS TLNPKQKQAL AKQLGLRARQ VEVWFQNRRA  180
RTKLKQTEVD CEFLRRCCEN LTEENRRLQK EVTELRALKL SPQFYMHMSP PTTLTMCPSC  240
EHVSAPPPQQ PPQAATSAQH HRGSLPVNAW AQGTRISHGL TFDALRPRS*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1127133SRKKLRL
2177185RRARTKLKQ
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
PlantRegMapCagra.0812s0021.1.p
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
GenBankAF3754530.0AF375453.1 Arabidopsis thaliana AT4g16780/dl4415w mRNA, complete cds.
GenBankATHHOMEOA0.0M90394.1 Arabidopsis thaliana heomeobox protein (HAT4) mRNA, complete cds.
GenBankAY0817470.0AY081747.1 Arabidopsis thaliana AT4g16780/dl4415w mRNA, complete cds.
GenBankX681450.0X68145.1 A.thaliana Athb-2 mRNA.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006284142.20.0homeobox-leucine zipper protein HAT4
SwissprotQ054661e-179HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLQ9LEM20.0Q9LEM2_9BRAS; Uncharacterized protein
STRINGCagra.0812s0021.1.p0.0(Capsella grandiflora)
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-162homeobox 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]