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_01845.1_g00006.1
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: 747aa    MW: 82108.6 Da    PI: 5.5293
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_01845.1_g00006.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox60.23.2e-1962117156
                              TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
                 Homeobox   1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                              +++ +++t+ q++eLe++F+++++p+ ++r+eL+++l+L+  q+k+WFqN+R+++k
  Rsa1.0_01845.1_g00006.1  62 KKRYHRHTQRQIQELESFFKECPHPDDKQRKELSRELNLEPLQIKFWFQNKRTQMK 117
                              688999***********************************************998 PP
2START209.99.7e-662604791206
                              HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S. CS
                    START   1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWdetla. 77 
                              ela +a++elv++a+ ++p+W +s    e++n++e+ ++f+++ +      ++ea+r+s+vv+m++ +lve+l+d++ qW+  +  
  Rsa1.0_01845.1_g00006.1 260 ELAVAAMEELVRMAQTGDPLWASSDssgEILNEEEYFRTFPRGIGpkpigMRSEASRESTVVIMNHINLVETLMDVN-QWSSVFCg 344
                              57899******************9999***************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++splvp R+ +fvRy++q+++ +w++vdvS+ds ++ +    + R++++pSg+l
  Rsa1.0_01845.1_g00006.1 345 ivsRALTLEVLSTGvagnynGALQVMTAEFQVPSPLVPtRENYFVRYCKQHSDSTWAVVDVSLDSLRPSQ----ITRSRRRPSGCL 426
                              999****************************************************************976....8*********** PP

                              EEEECTCEEEEEEEE-EE--SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
                    START 154 iepksnghskvtwvehvdlkgrlphwllrslvksglaegaktwvatlqrqcek 206
                              i++++ng+skvtwveh++ ++ ++h+++++lv++gla+gak+w+atl+rqce+
  Rsa1.0_01845.1_g00006.1 427 IQELQNGYSKVTWVEHTEFDDISVHAMYKPLVNTGLAFGAKRWLATLDRQCER 479
                              ***************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.603.9E-2243117IPR009057Homeodomain-like
SuperFamilySSF466891.04E-1851119IPR009057Homeodomain-like
PROSITE profilePS5007117.05459119IPR001356Homeobox domain
SMARTSM003896.2E-1860123IPR001356Homeobox domain
CDDcd000865.25E-1962120No hitNo description
PfamPF000467.9E-1762117IPR001356Homeobox domain
PROSITE patternPS00027094117IPR017970Homeobox, conserved site
PROSITE profilePS5084845.211251482IPR002913START domain
SuperFamilySSF559614.4E-35252481No hitNo description
CDDcd088756.05E-123255478No hitNo description
SMARTSM002341.5E-74260479IPR002913START domain
PfamPF018525.5E-55261479IPR002913START domain
Gene3DG3DSA:3.30.530.205.2E-5359473IPR023393START-like domain
SuperFamilySSF559611.48E-22499739No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009845Biological Processseed germination
GO:0009913Biological Processepidermal cell differentiation
GO:0048825Biological Processcotyledon development
GO:0090627Biological Processplant epidermal cell differentiation
GO:0005634Cellular Componentnucleus
GO:0008289Molecular Functionlipid binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 747 aa     Download sequence    Send to blast
MYHPNMFESH NHMFDMIKSS DNDLGLTGSR EDDFETKSGA EVTMENPLEE ELQDPNQRPN  60
KKKRYHRHTQ RQIQELESFF KECPHPDDKQ RKELSRELNL EPLQIKFWFQ NKRTQMKAQH  120
ERHDNSILKS DNDKLRAENN RYKDALSNAT CPNCGGPAAI GEMSFDEQHL KIENARLREE  180
IDRISAIAAK YVGKPMLAHS SPFSQLTSSH HIPSRSLDLE AGSFGNNNSQ TGFAGEMYRT  240
SDFMRSISIP CEADKPMIVE LAVAAMEELV RMAQTGDPLW ASSDSSGEIL NEEEYFRTFP  300
RGIGPKPIGM RSEASRESTV VIMNHINLVE TLMDVNQWSS VFCGIVSRAL TLEVLSTGVA  360
GNYNGALQVM TAEFQVPSPL VPTRENYFVR YCKQHSDSTW AVVDVSLDSL RPSQITRSRR  420
RPSGCLIQEL QNGYSKVTWV EHTEFDDISV HAMYKPLVNT GLAFGAKRWL ATLDRQCERL  480
ASSMANNIPT GDLSLITSPE GRKSMLKLAE RMVMSFCSGV GASTAHAWTT LAATGSDDVR  540
VMTRKSMDDP GRPPGIVLSA ATSFWIPVAP KRVFDFLRDE NCRSEWDILS NGGLVEEMAH  600
IANGRDPGNS VSLLRVNSSN SGQSNMLILQ ESCTDASGSY VIYAPVDMMA MNLVLSGGDP  660
DYVALLPSGF AILPDGSTSG GSAGAGAAGE VVTSTASNCG SLLTVAFQIL VDSVPTAKLS  720
LGSVATVNSL IKCTVQSIKD ALACDGA
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_01845.1_g00006.1
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_013630219.10.0PREDICTED: homeobox-leucine zipper protein MERISTEM L1-like
SwissprotQ8RWU40.0ATML1_ARATH; Homeobox-leucine zipper protein MERISTEM L1
TrEMBLA0A0D3BKU40.0A0A0D3BKU4_BRAOL; Uncharacterized protein
STRINGBo3g163910.10.0(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]