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_009135189.1
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: 761aa    MW: 83802.8 Da    PI: 5.9364
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009135189.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox60.23.3e-1963118156
                     TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
        Homeobox   1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                     +++ +++t+ q++eLe++F+++++p+ ++r+eL+++l+L+  q+k+WFqN+R+++k
  XP_009135189.1  63 KKRYHRHTQRQIQELESFFKECPHPDDKQRKELSRELNLEPLQIKFWFQNKRTQMK 118
                     688999***********************************************998 PP
2START200.47.9e-632604791206
                     HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S....EEEEEE CS
           START   1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWdetla....kaetle 83 
                     ela +a++elv++a+ ++p+W +     e++n++e+ + f+++ +     +++ea+r+s+vv+m++ +lve+l++++ q++  +     +a tle
  XP_009135189.1 260 ELAVAALEELVTMAQTGDPLWGLNDnlgEILNEEEYFRMFPRGIGpkpigFRSEASRESTVVIMNHINLVEILMNVN-QYSSVFCgivsRALTLE 353
                     57899*****************9999****************999********************************.99999988999****** 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+ +f+Ry++q+g+ +w++vdvS+d+ ++ p    + R++++pSg+li++++ng+skvtwveh++
  XP_009135189.1 354 VLSTGiagnynGALQVMTAEFQVPSPLVPtRENYFLRYCKQHGDNTWAVVDVSLDNLRPSP----ITRSRRRPSGCLIQELQNGYSKVTWVEHME 444
                     ***********************************************************99....7***************************** PP

                     --SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
           START 172 lkgrlphwllrslvksglaegaktwvatlqrqcek 206
                     +++r++h ++++lv++gla+gak+wvatl+rqce+
  XP_009135189.1 445 VDDRSVHTMYKPLVNTGLAFGAKRWVATLDRQCER 479
                     *********************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.601.3E-2147118IPR009057Homeodomain-like
SuperFamilySSF466891.34E-1853120IPR009057Homeodomain-like
PROSITE profilePS5007117.05460120IPR001356Homeobox domain
SMARTSM003896.2E-1861124IPR001356Homeobox domain
PfamPF000468.1E-1763118IPR001356Homeobox domain
CDDcd000865.44E-1963121No hitNo description
PROSITE patternPS00027095118IPR017970Homeobox, conserved site
PROSITE profilePS5084841.388251482IPR002913START domain
SuperFamilySSF559615.01E-35252481No hitNo description
CDDcd088756.52E-124255478No hitNo description
SMARTSM002348.1E-71260479IPR002913START domain
PfamPF018521.1E-51261479IPR002913START domain
Gene3DG3DSA:3.30.530.201.1E-6361478IPR023393START-like domain
SuperFamilySSF559611.22E-22499738No 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: 761 aa     Download sequence    Send to blast
MYHPNMFESH QHMFDMTPKE SGNDLGLTGS REDDFETKSG AEVTMENLLE EELQDPNQRP  60
NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRELN LEPLQIKFWF QNKRTQMKAQ  120
HERHDNSILK ADNDKLRAEN NRYKDALSNA TCPNCGGPAA IGEMSFDEQH LRIENARLRE  180
EIDRISSIAA KYVGKPLLPH SSPSTQLTSS HYIPSRSLGL EVGNFGTNHQ TSFVGEMHGT  240
SDIMRSVSIP CEADKPMIVE LAVAALEELV TMAQTGDPLW GLNDNLGEIL NEEEYFRMFP  300
RGIGPKPIGF RSEASRESTV VIMNHINLVE ILMNVNQYSS VFCGIVSRAL TLEVLSTGIA  360
GNYNGALQVM TAEFQVPSPL VPTRENYFLR YCKQHGDNTW AVVDVSLDNL RPSPITRSRR  420
RPSGCLIQEL QNGYSKVTWV EHMEVDDRSV HTMYKPLVNT GLAFGAKRWV ATLDRQCERL  480
ASSMASNIPT GDLSVITSPE GRKSMLKLAE RMVMSFFSGV GASTAHAWTT LATTGSDDVR  540
VMTRKSMDDP GRPPGIVLSA ATSFWIPVAP KRVFDFLRDE NSRSEWDILS NGGLVQKMAH  600
IANGRDPGNS ISLLRVNDTN SGPSNMLILQ ESCTDVSGSY VIYAPVDMTA MDVVLSGGDP  660
DYVALLPSGF AILPDGGEGG NASAGAEGGG NNRVVVNAGS LLTVAFQIIV DSVPTAKLSL  720
GSVATVNSLI KCTVERIKGA LACNATELDP SYSLKGGLGV F
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_009135189.1
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_009135189.10.0PREDICTED: homeobox-leucine zipper protein MERISTEM L1 isoform X2
SwissprotQ8RWU40.0ATML1_ARATH; Homeobox-leucine zipper protein MERISTEM L1
TrEMBLA0A3P5Z7I20.0A0A3P5Z7I2_BRACM; Uncharacterized protein
STRINGBo1g025510.10.0(Brassica oleracea)
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]