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 RrC10936_p1
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: 178aa    MW: 20110.3 Da    PI: 6.5066
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC10936_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox46.56.1e-153362356
                 SS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
     Homeobox 23 rypsaeereeLAkklgLterqVkvWFqNrRakek 56
                 +++  e++++LAkklgL+ rqV+vWFqNrRa++k
  RrC10936_p1  3 NKLEPERKTQLAKKLGLQPRQVSVWFQNRRARWK 36
                 678999***************************9 PP
2HD-ZIP_I/II102.83e-332742193
  HD-ZIP_I/II 21 eekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreelke 93
                 e+kLeperK++la++Lglqprqv vWFqnrRAR+ktkqlE+d++ Lk++yd+l ++ +++ k++++Lr+++++
  RrC10936_p1  2 ENKLEPERKTQLAKKLGLQPRQVSVWFQNRRARWKTKQLERDFNLLKSSYDQLLSNYDSILKDNHHLRSQVTS 74
                 79*******************************************************************9975 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM003890.0019142IPR001356Homeobox domain
PROSITE profilePS5007113.993138IPR001356Homeobox domain
PfamPF000463.0E-12336IPR001356Homeobox domain
SuperFamilySSF466892.57E-13349IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.602.3E-15344IPR009057Homeodomain-like
CDDcd000864.07E-12739No hitNo description
PRINTSPR000311.5E-6918IPR000047Helix-turn-helix motif
PROSITE patternPS0002701336IPR017970Homeobox, conserved site
PRINTSPR000311.5E-61834IPR000047Helix-turn-helix motif
PfamPF021832.4E-163880IPR003106Leucine zipper, homeobox-associated
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0001558Biological Processregulation of cell growth
GO:0009637Biological Processresponse to blue light
GO:0009651Biological Processresponse to salt stress
GO:0009965Biological Processleaf morphogenesis
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
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: 178 aa     Download sequence    Send to blast
MENKLEPERK TQLAKKLGLQ PRQVSVWFQN RRARWKTKQL ERDFNLLKSS YDQLLSNYDS  60
ILKDNHHLRS QVTSLAGKVQ AKEETATGQV PEPNQLDPVN MNPAIKTEDR LSSGSAVLDE  120
DAPHQLRDSC DSYFPSIVPI HHHSGQDTNN NNGCGNDTGC FADVFVQGES FGLWGCWT
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
13038RRARWKTKQ
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription activator involved in leaf development. Binds to the DNA sequence 5'-CAAT[AT]ATTG-3'. {ECO:0000269|PubMed:8535134}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00323DAPTransfer from AT3G01470Download
Motif logo
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3528542e-79AK352854.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-08-H09.
GenBankAK3535352e-79AK353535.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-50-D05.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018488766.11e-131PREDICTED: homeobox-leucine zipper protein HAT5-like
SwissprotQ022834e-82HAT5_ARATH; Homeobox-leucine zipper protein HAT5
TrEMBLA0A3P5Z3871e-109A0A3P5Z387_BRACM; Uncharacterized protein
STRINGBra039116.1-P1e-110(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM88842738
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G01470.16e-79homeobox 1
Publications ? help Back to Top
  1. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  2. Ribone PA,Capella M,Arce AL,Chan RL
    A uORF Represses the Transcription Factor AtHB1 in Aerial Tissues to Avoid a Deleterious Phenotype.
    Plant Physiol., 2017. 175(3): p. 1238-1253
    [PMID:28956754]