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 GSBRNA2T00106768001
Common NameGSBRNA2T00106768001
Organism
Brassica napus
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: 696aa    MW: 77143.3 Da    PI: 6.245
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00106768001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox61.61.2e-1963118156
                          TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
             Homeobox   1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                          +++ +++t+ q++eLe++F+++++p+ ++r+eL+++l+L+  qVk+WFqN+R+++k
  GSBRNA2T00106768001  63 KKRYHRHTQRQIQELESFFKECPHPDDKQRKELSRELNLEPLQVKFWFQNKRTQMK 118
                          688999***********************************************998 PP
2START216.77.8e-682164351206
                          HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S....E CS
                START   1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWdetla....k 78 
                          ela +a++elv++a+ ++p+Wv+s    e++n++e+ ++f+++ +      ++ea+r+s+vv+m++ +lve+l+d++ qW+  +     +
  GSBRNA2T00106768001 216 ELAVAAMEELVRMAQTGDPLWVSSDnavEILNEEEYFRTFPRGIGpkplgLRSEASRESTVVIMNHINLVEILMDVN-QWSSVFCgivsR 304
                          57899*************************************999********************************.******99999* PP

                          EEEEEEECTT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCE CS
                START  79 aetlevissg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksngh 161
                          a tlev+s+g      galq+m+ae+q++splvp R+ +fvRy++q+++ +w++vdvS+ds ++ p    + R +++pSg+li++++ng+
  GSBRNA2T00106768001 305 ALTLEVLSTGvagnynGALQVMTAEFQVPSPLVPtRENYFVRYCKQHSDNTWAVVDVSLDSLRPSP----ITRNRRRPSGCLIQELQNGY 390
                          ****************************************************************99....6******************* PP

                          EEEEEEE-EE--SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
                START 162 skvtwvehvdlkgrlphwllrslvksglaegaktwvatlqrqcek 206
                          skvtwveh+++++r++h ++++lv++gla+gak+wvatl+rqce+
  GSBRNA2T00106768001 391 SKVTWVEHTEVDDRSVHTMYKPLVNTGLAFGAKRWVATLDRQCER 435
                          *******************************************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-2244118IPR009057Homeodomain-like
SuperFamilySSF466895.13E-1952120IPR009057Homeodomain-like
PROSITE profilePS5007117.15160120IPR001356Homeobox domain
SMARTSM003893.9E-1861124IPR001356Homeobox domain
PfamPF000462.9E-1763118IPR001356Homeobox domain
CDDcd000865.47E-1963121No hitNo description
PROSITE patternPS00027095118IPR017970Homeobox, conserved site
PROSITE profilePS5084844.966207438IPR002913START domain
SuperFamilySSF559613.3E-35208437No hitNo description
CDDcd088751.80E-124211434No hitNo description
SMARTSM002347.6E-79216435IPR002913START domain
PfamPF018527.7E-57217435IPR002913START domain
Gene3DG3DSA:3.30.530.201.1E-5315434IPR023393START-like domain
SuperFamilySSF559611.51E-24455687No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0008289Molecular Functionlipid binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 696 aa     Download sequence    Send to blast
MYQPNMFESH HHMFDMTPKN SDNDLGLTGS REDDFETKSG AEVTMENPLE EELQDPNQRP  60
NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRELN LEPLQVKFWF QNKRTQMKAQ  120
HERHENSILK SDNDKLRAEN NRIENARLRE EIDRISAIAA KYVGKPLLTH SSSSFPQLTS  180
SHHIPQTGFL GDMYGTSDIM RSVSIHNDAD KPMIVELAVA AMEELVRMAQ TGDPLWVSSD  240
NAVEILNEEE YFRTFPRGIG PKPLGLRSEA SRESTVVIMN HINLVEILMD VNQWSSVFCG  300
IVSRALTLEV LSTGVAGNYN GALQVMTAEF QVPSPLVPTR ENYFVRYCKQ HSDNTWAVVD  360
VSLDSLRPSP ITRNRRRPSG CLIQELQNGY SKVTWVEHTE VDDRSVHTMY KPLVNTGLAF  420
GAKRWVATLD RQCERLASSM ASNIPTGDLS VITSPEGRKS MLKLAERMVM SFCSGVGASN  480
AHAWTTLATT GSDDVRVMTR KSMDDPGRPP GIVLSAATSF WIPVAPKRVF DFLRDENSRS  540
EWDILSNGGL VQEMAHIANG RDPGNSVSLF RVNSANSGQS NMLILQESCT DASGSYVIYA  600
PVDIMAMNVV LSGGDPDYVA LLPSGFAILP DGSSRVNAMV TSTASNCGSL LTVAFQILVD  660
SVPTAKLSLG SVATVNSLIK CTVERIKAAL ACDGA*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bna.125736e-84leaf
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
PlantRegMapGSBRNA2T00106768001
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_013696499.10.0homeobox-leucine zipper protein MERISTEM L1
RefseqXP_013696501.10.0homeobox-leucine zipper protein MERISTEM L1
RefseqXP_013696503.10.0homeobox-leucine zipper protein MERISTEM L1 isoform X2
RefseqXP_022546647.10.0homeobox-leucine zipper protein MERISTEM L1 isoform X1
RefseqXP_022546648.10.0homeobox-leucine zipper protein MERISTEM L1
SwissprotQ8RWU40.0ATML1_ARATH; Homeobox-leucine zipper protein MERISTEM L1
TrEMBLM4FCD80.0M4FCD8_BRARP; Uncharacterized protein
STRINGBra038757.1-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. Chalhoub B, et al.
    Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.
    Science, 2014. 345(6199): p. 950-3
    [PMID:25146293]
  4. 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]
  5. 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]
  6. 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]
  7. Schwarz EM,Roeder AH
    Transcriptomic Effects of the Cell Cycle Regulator LGO in Arabidopsis Sepals.
    Front Plant Sci, 2016. 7: p. 1744
    [PMID:27920789]
  8. Meyer HM, et al.
    Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal.
    Elife, 2018.
    [PMID:28145865]