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 XP_009137213.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family HD-ZIP
Protein Properties Length: 755aa    MW: 83320.6 Da    PI: 5.9134
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009137213.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox603.7e-1963118156
                     TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
        Homeobox   1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                     +++ +++t+ q++eLe++F+++++p+ ++r+eL+++l+L+  qVk+WF+N+R+++k
  XP_009137213.1  63 KKRYHRHTQRQIQELESFFKECPHPDDKQRKELSRELNLEPLQVKFWFHNKRTQMK 118
                     688999***********************************************998 PP
2START216.58.8e-682634821206
                     HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S....EEEEEE CS
           START   1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWdetla....kaetle 83 
                     ela +a++elv++a+ ++p+Wv+s    e++n++e+ ++f+++ +      ++ea+r+s+vv+m++ +lve+l+d++ qW+  +     +a tle
  XP_009137213.1 263 ELAVAAMEELVRMAQTGDPLWVSSDsavEILNEEEYFRTFPRGIGpkplgLRSEASRESTVVIMNHINLVEILMDVN-QWSSVFCgivsRALTLE 356
                     57899*******************999***************999********************************.******99999****** PP

                     EECTT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE CS
           START  84 vissg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghskvtwvehvd 171
                     v+s+g      galq+m+ae+q++splvp R+ +fvRy++q+++ +w++vdvS+ds ++ p    + R +++pSg+li++++ng+skvtwveh++
  XP_009137213.1 357 VLSTGvagnynGALQVMTAEFQVPSPLVPtRENYFVRYCKQHSDNTWAVVDVSLDSLRPSP----ITRNRRRPSGCLIQELQNGYSKVTWVEHTE 447
                     ***********************************************************99....6***************************** PP

                     --SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
           START 172 lkgrlphwllrslvksglaegaktwvatlqrqcek 206
                     +++r++h ++++lv++gla+gak+wvatl+rqce+
  XP_009137213.1 448 VDDRSVHTMYKPLVNTGLAFGAKRWVATLDRQCER 482
                     *********************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.609.7E-2244118IPR009057Homeodomain-like
SuperFamilySSF466894.71E-1852120IPR009057Homeodomain-like
PROSITE profilePS5007116.68260120IPR001356Homeobox domain
SMARTSM003895.4E-1761124IPR001356Homeobox domain
PfamPF000468.4E-1763118IPR001356Homeobox domain
CDDcd000868.41E-1863121No hitNo description
PROSITE patternPS00027095118IPR017970Homeobox, conserved site
PROSITE profilePS5084845.064254485IPR002913START domain
SuperFamilySSF559615.22E-35255484No hitNo description
CDDcd088751.41E-124258481No hitNo description
SMARTSM002343.4E-78263482IPR002913START domain
PfamPF018528.7E-57264482IPR002913START domain
Gene3DG3DSA:3.30.530.201.2E-5362481IPR023393START-like domain
SuperFamilySSF559614.6E-24502681No hitNo description
SuperFamilySSF559614.6E-24708747No 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: 755 aa     Download sequence    Send to blast
MYQPNMFESH HHMFDMTPKN SDNDLGLTGS REDDFETKSG AEVTMENPLE EELQDPNQRP  60
NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRELN LEPLQVKFWF HNKRTQMKAQ  120
HERHENSILK SYNDKLRAEN NRYKDAINNE TCQNCGGPAA IGXMSFAEQH LRIENARLSE  180
EIDRISAIAT KYVGKPLLTH SSSSFPQLTS SHHIPSRSLD LEVGNFGNTN NSQTGFLGDM  240
YGTSDIMRSV SIHNDADKPM IVELAVAAME ELVRMAQTGD PLWVSSDSAV EILNEEEYFR  300
TFPRGIGPKP LGLRSEASRE STVVIMNHIN LVEILMDVNQ WSSVFCGIVS RALTLEVLST  360
GVAGNYNGAL QVMTAEFQVP SPLVPTRENY FVRYCKQHSD NTWAVVDVSL DSLRPSPITR  420
NRRRPSGCLI QELQNGYSKV TWVEHTEVDD RSVHTMYKPL VNTGLAFGAK RWVATLDRQC  480
ERLASSMASN IPTGDLSVIT SPEGRKSMLK LAERMVMSFC SGVGASNAHA WTTLATTGSD  540
DVRVMTRKSM DDPGRPPGIV LSAATSFWIP VAPKRVFDFL RDENSRSEWD ILSNGGLVQE  600
MAHIANGRDP GNSVSLFRVN SANSGQSNML ILQESCTDAS GSYVIYAPVD IMAMNVVLSG  660
GDPDYVALLP SGFAILPDGS SRVNASAGAE GGDGNNLEVV TSTASNCGSL LTVAFQILVD  720
SVPTAKLSLG SVATVNSLIK CTVERIKAAL ACDGA
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: First expressed in the apical cell after the first asymmetric division of the zygote. Expressed in all proembryo cells until the eight-cell stage, and then restricted to the protoderm in the 16-cell proembryo. Not detected in the torpedo stage, but reappeared later in the L1 layer of the shoot apical meristem in the mature embryo. After germination, the L1 layer-specific expression pattern is maintained in the vegetative shoot apical meristem, inflorescence, floral meristems, and the young floral organ primordia. Finally, expressed in the protoderm of the ovule primordia and integuments and gradually restricted to the endothelium surrounding the embryo sac. {ECO:0000269|PubMed:10571886, ECO:0000269|PubMed:8989876}.
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
PlantRegMapXP_009137213.1
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_009137213.10.0PREDICTED: LOW QUALITY PROTEIN: homeobox-leucine zipper protein MERISTEM L1-like
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]