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 Carubv10005275m
Common NameCARUB_v10005275mg
Organism
Capsella rubella
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: 319aa    MW: 35709.1 Da    PI: 10.0092
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10005275mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox60.72.3e-19158212256
                      T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
         Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                      rk+ +++k+q  +Lee F+ +++++ ++++ LAk+lgL  rqV vWFqNrRa+ k
  Carubv10005275m 158 RKKLRLSKDQSAILEETFKDHSTLNPKQKQALAKQLGLRARQVEVWFQNRRARTK 212
                      788899***********************************************98 PP
2HD-ZIP_I/II1246.9e-40158247191
      HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreel 91 
                      +kk+rlsk+q+++LEe+F+ +++L+p++K++la++Lgl++rqv+vWFqnrRARtk+kq+E+d+e+L+r++++l+een+rL+kev+eLr +l
  Carubv10005275m 158 RKKLRLSKDQSAILEETFKDHSTLNPKQKQALAKQLGLRARQVEVWFQNRRARTKLKQTEVDCEFLRRCCENLTEENRRLQKEVTELR-AL 247
                      69*************************************************************************************9.55 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046185.0E-2731136IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.603.5E-18127215IPR009057Homeodomain-like
PROSITE profilePS5007117.427154214IPR001356Homeobox domain
SuperFamilySSF466895.56E-18156223IPR009057Homeodomain-like
SMARTSM003895.2E-16156218IPR001356Homeobox domain
PfamPF000469.3E-17158212IPR001356Homeobox domain
CDDcd000862.78E-14158215No hitNo description
PRINTSPR000311.4E-5185194IPR000047Helix-turn-helix motif
PROSITE patternPS000270189212IPR017970Homeobox, conserved site
PRINTSPR000311.4E-5194210IPR000047Helix-turn-helix motif
PfamPF021839.7E-11214248IPR003106Leucine zipper, homeobox-associated
SMARTSM003403.8E-26214257IPR003106Leucine 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: 319 aa     Download sequence    Send to blast
SLSISQKKEK SRKLYCKNRV FLFVPEKIKM MLEKDDLGLS LGLNYPKKQM NLNSNPSVSV  60
TPSSSSFGLL RRSSLNESFT SSVPNSDSSQ KEKRTFIRGI DVNRPPSTAE YGEEDAGVSS  120
PNSTVSSSTG KRSEREEDTD PQGSRGGISD DEDGDNSRKK LRLSKDQSAI LEETFKDHST  180
LNPKQKQALA KQLGLRARQV EVWFQNRRAR TKLKQTEVDC EFLRRCCENL TEENRRLQKE  240
VTELRALKLS PQFYMHMSPP TTLTMCPSCE HVSAPPPQQP PQAATSAQHH RGSLPVNAWA  300
QGTRISHGLT FDALRPRS*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1156162SRKKLRL
2206214RRARTKLKQ
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
PlantRegMapCarubv10005275m
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.
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-178HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLR0GXM30.0R0GXM3_9BRAS; Uncharacterized protein (Fragment)
STRINGXP_006284142.10.0(Capsella rubella)
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]