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 Rsa1.0_00115.1_g00017.1
Organism
Raphanus sativus
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: 739aa    MW: 81406.6 Da    PI: 4.9797
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_00115.1_g00017.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox59.74.7e-1955106556
                              SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
                 Homeobox   5 ttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                              +++t+ q++eLe++F+++++p+ ++r+eL++ l+L+  qVk+WFqN+R+++k
  Rsa1.0_00115.1_g00017.1  55 HRHTQRQIQELESFFKECPHPDDKQRKELSRDLNLEPLQVKFWFQNKRTQMK 106
                              689**********************************************998 PP
2START210.65.8e-662504691206
                              HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S. CS
                    START   1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWdetla. 77 
                              ela +a++elv++a+ ++p+Wv+s    e++n++e+ ++f+++ +     +++ea+r+s+vv+m++ +lve+l+d++ qW+  +  
  Rsa1.0_00115.1_g00017.1 250 ELAVAAMEELVTMAQTGDPLWVSSDnlgEILNEEEYFRTFPRGIGpkpigFRSEASRESTVVIMNHINLVEILMDVN-QWSSVFCg 334
                              57899*************************************999********************************.******99 PP

                              ...EEEEEEEECTT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEE CS
                    START  78 ...kaetlevissg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgil 153
                                 +a tlev+s g      galq+m+ae+q++splv  R+++fvRy++q+g+ +w++vdvS+ds ++ p    + R++++pSg+l
  Rsa1.0_00115.1_g00017.1 335 ivsRALTLEVLSAGvagnynGALQVMTAEFQVPSPLVQiRESYFVRYCKQHGDNTWAVVDVSLDSLSPSP----ITRSRRRPSGCL 416
                              999*****************************************************************99....7*********** PP

                              EEEECTCEEEEEEEE-EE--SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
                    START 154 iepksnghskvtwvehvdlkgrlphwllrslvksglaegaktwvatlqrqcek 206
                              i++++ng+skvtwveh+++++ ++h ++++lv++gla+gak+wvatl+rqce+
  Rsa1.0_00115.1_g00017.1 417 IQELQNGYSKVTWVEHMEVEDTSVHTMYKPLVNTGLAFGAKRWVATLDRQCER 469
                              ***************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.602.2E-2132106IPR009057Homeodomain-like
SuperFamilySSF466892.67E-1840108IPR009057Homeodomain-like
PROSITE profilePS5007116.76348108IPR001356Homeobox domain
SMARTSM003892.3E-1749112IPR001356Homeobox domain
CDDcd000863.34E-1850109No hitNo description
PfamPF000461.1E-1655106IPR001356Homeobox domain
PROSITE patternPS00027083106IPR017970Homeobox, conserved site
PROSITE profilePS5084844.427241472IPR002913START domain
SuperFamilySSF559613.43E-35242471No hitNo description
CDDcd088754.31E-124245468No hitNo description
SMARTSM002344.0E-72250469IPR002913START domain
PfamPF018523.6E-55251469IPR002913START domain
Gene3DG3DSA:3.30.530.204.5E-7345464IPR023393START-like domain
SuperFamilySSF559611.03E-23489730No hitNo description
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: 739 aa     Download sequence    Send to blast
MFDMTPKESD NDLGLTGSRE DDFETKSGAE VTMDNQLEEE LQDPNHRPNK KKRFHRHTQR  60
QIQELESFFK ECPHPDDKQR KELSRDLNLE PLQVKFWFQN KRTQMKAQHE RHENSILKTD  120
NDKLRAENNR YKDALSNATC SNCGCLSIGE VSFDEQHLRI ENARLREEID RISAMAAKYV  180
GKPSSSHSSP STQLTSSHYI PSRSLDPEVG NFGTNNNDHQ TSFVGEMYGT SDVMRSVSIP  240
CEADKPMIVE LAVAAMEELV TMAQTGDPLW VSSDNLGEIL NEEEYFRTFP RGIGPKPIGF  300
RSEASRESTV VIMNHINLVE ILMDVNQWSS VFCGIVSRAL TLEVLSAGVA GNYNGALQVM  360
TAEFQVPSPL VQIRESYFVR YCKQHGDNTW AVVDVSLDSL SPSPITRSRR RPSGCLIQEL  420
QNGYSKVTWV EHMEVEDTSV HTMYKPLVNT GLAFGAKRWV ATLDRQCERF ASSMASNIPT  480
GDLSVITSPE GRKSMLKLAE RMVMSFCSGV GASTANAWTT LTTTGSDDVR VMTRKSMDDP  540
GRPPGIVLSA ATSFWIPVAP KRVFDFLRDE NSRSEWDILS NGGLVQEMAH IANGRDPGNS  600
VSLLRVNGTN SGQSNMLILQ ESCTDASGSY VIYAPVDVAA MNVVMNGGDP EYVVLFPSGF  660
AILPDGSTRE GGNASAVAGG GGNNLEVVNS GSLLTVAFQI LVDSVPTVKL SLGSVATVNS  720
LIKCTVELIK GALAWEELD
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_00115.1_g00017.1
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_018469534.10.0PREDICTED: homeobox-leucine zipper protein MERISTEM L1-like
SwissprotQ8RWU40.0ATML1_ARATH; Homeobox-leucine zipper protein MERISTEM L1
TrEMBLA0A3P5Z7I20.0A0A3P5Z7I2_BRACM; Uncharacterized protein
STRINGBo1g025510.10.0(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]