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_009108529.1
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: 748aa    MW: 82403.9 Da    PI: 5.3456
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009108529.1genomeNCBIView 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
  XP_009108529.1  62 KKRYHRHTQRQIQELESFFKECPHPDDKQRKELSRELNLEPLQIKFWFQNKRTQMK 117
                     688999***********************************************998 PP
2START206.41.1e-642614801206
                     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+de+ ++f+++ +      ++ea+r+s+vv+m++ +lve+l+d++ qW+  +     +a tl+
  XP_009108529.1 261 ELAVAAMEELVRMAQTGDPLWVSSDssgEILNEDEYFRTFPRGIGpkpigLRSEASRESTVVIMNQINLVEILMDVN-QWSSVFCgivsRALTLD 354
                     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+ +ae+q+ splvp R+ +fvRy++q+++ +w++vdvS++s ++ p    + R++++pSg++i++++ng+skvtwveh++
  XP_009108529.1 355 VLSTGvagnynGALQVLTAEFQVQSPLVPtRENYFVRYCKQHSDTTWAVVDVSLESLRPSP----ITRSRRRPSGCVIQELQNGYSKVTWVEHTE 445
                     ***********************************************************99....7***************************** PP

                     --SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
           START 172 lkgrlphwllrslvksglaegaktwvatlqrqcek 206
                     +++ ++h ++++lv+ gla+gak+wvatl+rqce+
  XP_009108529.1 446 VDDISVHTMYKPLVNAGLAFGAKRWVATLDRQCER 480
                     *********************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.601.7E-2245117IPR009057Homeodomain-like
SuperFamilySSF466897.1E-1951119IPR009057Homeodomain-like
PROSITE profilePS5007117.05459119IPR001356Homeobox domain
SMARTSM003896.2E-1860123IPR001356Homeobox domain
CDDcd000865.26E-1962120No hitNo description
PfamPF000467.9E-1762117IPR001356Homeobox domain
PROSITE patternPS00027094117IPR017970Homeobox, conserved site
PROSITE profilePS5084844.476252483IPR002913START domain
SuperFamilySSF559615.91E-33254482No hitNo description
CDDcd088751.28E-119256479No hitNo description
SMARTSM002346.3E-74261480IPR002913START domain
PfamPF018525.2E-54262480IPR002913START domain
Gene3DG3DSA:3.30.530.209.5E-6361479IPR023393START-like domain
SuperFamilySSF559611.76E-21500741No 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: 748 aa     Download sequence    Send to blast
MYHPNMFESH HHMFDMTKSS DNDLGLTGSR EDDFETKSGA EVTLDNPLEE ELQDPDQRPN  60
KKKRYHRHTQ RQIQELESFF KECPHPDDKQ RKELSRELNL EPLQIKFWFQ NKRTQMKAQH  120
ERHENSILKS DNDKLRAENN RYKDALSNAT CPNCGGPAAI GEMSFDEQHL RIENARLHEE  180
IDRISFIAAK YVGKPMLPHS SPFSQLTTST HIPTRSLDLE VGSFGNNNSS QTGFVGDIYG  240
TNDIMRSVSI PCESDKPMIV ELAVAAMEEL VRMAQTGDPL WVSSDSSGEI LNEDEYFRTF  300
PRGIGPKPIG LRSEASREST VVIMNQINLV EILMDVNQWS SVFCGIVSRA LTLDVLSTGV  360
AGNYNGALQV LTAEFQVQSP LVPTRENYFV RYCKQHSDTT WAVVDVSLES LRPSPITRSR  420
RRPSGCVIQE LQNGYSKVTW VEHTEVDDIS VHTMYKPLVN AGLAFGAKRW VATLDRQCER  480
LASSMASNIP TGDLSVITSP EGRKSMLKLA ERMVMSFCSG VGASTAHAWS TLAATGSDDV  540
RVMTRKSMDD PGRPPGIVLS AATSFWIPMG LKRVFDFLRD ENSRSQWDIL SNGGLVEEMA  600
HIANGRDPGN SVSLLRVNSS NSGESNMLIL QESCTDASGS YVIYAPVDMM AMNVVLSGGD  660
PDYVALLPSG FAILPDGSTR GGNASVVAEG EVVTSTASNC GSLLTVAFQI LVDSVPTAKL  720
SLGSVATVNS LIKCTVQRIK DALACDGA
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_009108529.1
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_009108529.10.0PREDICTED: homeobox-leucine zipper protein MERISTEM L1-like
RefseqXP_018509149.10.0PREDICTED: homeobox-leucine zipper protein MERISTEM L1-like
SwissprotQ8RWU40.0ATML1_ARATH; Homeobox-leucine zipper protein MERISTEM L1
TrEMBLM4DWH80.0M4DWH8_BRARP; Uncharacterized protein
STRINGBra020872.1-P0.0(Brassica rapa)
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]