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 RrC3699_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: 343aa    MW: 39291.9 Da    PI: 5.5784
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC3699_p2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox62.65.8e-2063118156
                 TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
    Homeobox   1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                 +++ +++t+ q++eLe++F+++++p+ ++r+eL+++l+L+  qVk+WFqN+R+++k
  RrC3699_p2  63 KKRYHRHTQRQIQELESFFKECPHPDDKQRKELSRELNLEPLQVKFWFQNKRTQMK 118
                 678899***********************************************998 PP
2START461.5e-15263342173
                 HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT- CS
       START   1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWd 73 
                 ela +a++elv++a+ ++p+Wv s    e++ ++e+ ++f+++ +      ++ea+r+s+vv+m++ +lve+l+d++ qW+
  RrC3699_p2 263 ELAVAAMEELVRMAQTGDPLWVPSDnavEILSEEEYFRTFPRGIGpkpigLRSEASRESTVVIMNHINLVEILMDVN-QWS 342
                 57899******************9999***************999********************************.**7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.605.7E-2344118IPR009057Homeodomain-like
SuperFamilySSF466891.75E-1952120IPR009057Homeodomain-like
PROSITE profilePS5007117.15160120IPR001356Homeobox domain
SMARTSM003893.9E-1861124IPR001356Homeobox domain
PfamPF000461.4E-1763118IPR001356Homeobox domain
CDDcd000862.68E-1863121No hitNo description
PROSITE patternPS00027095118IPR017970Homeobox, conserved site
PROSITE profilePS5084815.758254343IPR002913START domain
PfamPF018522.9E-9264342IPR002913START domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0008289Molecular Functionlipid binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 343 aa     Download sequence    Send to blast
MYQPNMFESH HHMFDMTPKN SDNDLGLTGS REDDFETKSG AEVTMENPLE EELQDPNQRP  60
NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRELN LEPLQVKFWF QNKRTQMKAQ  120
HERHENSILK SDNDKLRAEN NRYKDALNNA TCPNCGGPAA IGEMSFDEQH LRIENARLRE  180
EIDRISAIAA KYVGKPLLTH SSSSFPQLTS SHHIPSRSLD LEVGNFGNTN TSQTGFLGDM  240
YGTSDIMRSV SIHNDADKPM IVELAVAAME ELVRMAQTGD PLWVPSDNAV EILSEEEYFR  300
TFPRGIGPKP IGLRSEASRE STVVIMNHIN LVEILMDVNQ WSS
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in cell specification and pattern formation during embryogenesis. Binds to the L1 box DNA sequence 5'-TAAATG[CT]A-3'. Plays a role in maintaining the identity of L1 cells, possibly by interacting with their L1 box or other target-gene promoters. Functionally redundant to PDF2. {ECO:0000269|PubMed:11439135, ECO:0000269|PubMed:12505995}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2299700.0AK229970.1 Arabidopsis thaliana mRNA for L1 specific homeobox gene ATML1/ovule-specific homeobox protein A20, complete cds, clone: RAFL22-43-B20.
GenBankAY0911040.0AY091104.1 Arabidopsis thaliana putative L1-specific homeobox gene ATML1/ovule-specific homeobox protein A20 (At4g21750) mRNA, complete cds.
GenBankAY1504910.0AY150491.1 Arabidopsis thaliana putative L1-specific homeobox gene ATML1/ovule-specific homeobox protein A20 (At4g21750) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013696499.10.0homeobox-leucine zipper protein MERISTEM L1
RefseqXP_013696501.10.0homeobox-leucine zipper protein MERISTEM L1
RefseqXP_013696503.10.0homeobox-leucine zipper protein MERISTEM L1 isoform X2
RefseqXP_022546647.10.0homeobox-leucine zipper protein MERISTEM L1 isoform X1
RefseqXP_022546648.10.0homeobox-leucine zipper protein MERISTEM L1
SwissprotQ8RWU40.0ATML1_ARATH; Homeobox-leucine zipper protein MERISTEM L1
TrEMBLA0A3P6ADA30.0A0A3P6ADA3_BRACM; Uncharacterized protein
STRINGBo7g107550.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM49128149
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G21750.20.0HD-ZIP family protein
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. Takada S,Takada N,Yoshida A
    Induction of epidermal cell fate in Arabidopsis shoots.
    Plant Signal Behav, 2013. 8(11): p. e26236
    [PMID:23989220]
  3. Liang Z,Brown RC,Fletcher JC,Opsahl-Sorteberg HG
    Calpain-Mediated Positional Information Directs Cell Wall Orientation to Sustain Plant Stem Cell Activity, Growth and Development.
    Plant Cell Physiol., 2015. 56(9): p. 1855-66
    [PMID:26220906]
  4. Katagiri Y, et al.
    The coordination of ploidy and cell size differs between cell layers in leaves.
    Development, 2016. 143(7): p. 1120-5
    [PMID:26903507]
  5. Seeliger I, et al.
    The AP2-type transcription factors DORNRÖSCHEN and DORNRÖSCHEN-LIKE promote G1/S transition.
    Mol. Genet. Genomics, 2016. 291(5): p. 1835-49
    [PMID:27277595]
  6. Schwarz EM,Roeder AH
    Transcriptomic Effects of the Cell Cycle Regulator LGO in Arabidopsis Sepals.
    Front Plant Sci, 2016. 7: p. 1744
    [PMID:27920789]
  7. Meyer HM, et al.
    Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal.
    Elife, 2018.
    [PMID:28145865]