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 RrC8416_p2
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family HD-ZIP
Protein Properties Length: 237aa    MW: 25535.6 Da    PI: 8.2917
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC8416_p2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox57.72e-1895149256
                 T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
    Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                 rk+ +++keq  +Lee F+++++++ +++  LAk+l+L +rqV vWFqNrRa+ k
  RrC8416_p2  95 RKKLRLSKEQALVLEETFKQHSTLNPKQKLALAKQLNLRTRQVEVWFQNRRARTK 149
                 778899***********************************************98 PP
2HD-ZIP_I/II123.88.3e-4095184191
  HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreel 91 
                  +kk+rlskeq+ +LEe+F+++++L+p++K +la++L+l++rqv+vWFqnrRARtk+kq+E+d+e+Lkr++d+l+een+rL+kev+eLr +l
   RrC8416_p2  95 RKKLRLSKEQALVLEETFKQHSTLNPKQKLALAKQLNLRTRQVEVWFQNRRARTKLKQTEVDCEYLKRCCDSLTEENRRLHKEVSELR-AL 184
                  69*************************************************************************************9.55 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046181.1E-14454IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.603.2E-1975149IPR009057Homeodomain-like
SuperFamilySSF466894.71E-1979152IPR009057Homeodomain-like
PROSITE profilePS5007116.94191151IPR001356Homeobox domain
SMARTSM003893.4E-1593155IPR001356Homeobox domain
PfamPF000466.7E-1695149IPR001356Homeobox domain
CDDcd000864.79E-1695152No hitNo description
PROSITE patternPS000270126149IPR017970Homeobox, conserved site
SMARTSM003408.7E-27151194IPR003106Leucine zipper, homeobox-associated
PfamPF021835.9E-12151185IPR003106Leucine zipper, homeobox-associated
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009641Biological Processshade avoidance
GO:0009725Biological Processresponse to hormone
GO:0010218Biological Processresponse to far red light
GO:0005634Cellular Componentnucleus
GO:0009506Cellular Componentplasmodesma
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 237 aa     Download sequence    Send to blast
MLSVERNSDV GSFLRGSNVN RTPSAAVVIN LEEDVAGMSS PNSTVSTVSG NKRDLAATRG  60
DGGVDENDAE KASCSHGGGS GGSDEEEGGN CDGTRKKLRL SKEQALVLEE TFKQHSTLNP  120
KQKLALAKQL NLRTRQVEVW FQNRRARTKL KQTEVDCEYL KRCCDSLTEE NRRLHKEVSE  180
LRALKLSPHL YMHMTPPTTL TMCPSCERVS ASSSSSAMAA ATPPPSTASG GGGRIPT
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
19399TRKKLRL
2143151RRARTKLKQ
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor. {ECO:0000250}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By transition from light to far-red light. {ECO:0000269|PubMed:8106086}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018465539.11e-145PREDICTED: homeobox-leucine zipper protein ATHB-4-like
SwissprotP929531e-109ATHB4_ARATH; Homeobox-leucine zipper protein ATHB-4
TrEMBLA0A3P6CBY51e-130A0A3P6CBY5_BRACM; Uncharacterized protein
STRINGBra040335.1-P1e-129(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM25772772
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G44910.12e-95homeobox-leucine zipper protein 4
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. 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]
  3. Gallemí M, et al.
    A non-DNA-binding activity for the ATHB4 transcription factor in the control of vegetation proximity.
    New Phytol., 2017. 216(3): p. 798-813
    [PMID:28805249]