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_009122816.1
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 TALE
Protein Properties Length: 633aa    MW: 68399 Da    PI: 8.137
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009122816.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox27.94.1e-094204522254
                     SSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHH CS
        Homeobox  22 nrypsaeereeLAkklgLterqVkvWFqNrRak 54 
                     ++yp+ +++  LAk++gL+ +qV++WF N R +
  XP_009122816.1 420 HPYPTDTDKLMLAKQTGLSRNQVSNWFINARVR 452
                     89*****************************87 PP
2BELL107.39.5e-35274341572
            BELL   5 lqkkkakLlslleeVdkrYkqyveqlqtvissFeavaglgsakpYtslAlkaiSrhFrcLkdaiaeqi 72 
                       k k+kL+s+l+eV+krYkqy+eqlq+v++sFe+vaglg+a+pY+sl lka+SrhF+cLk+ai+eq+
  XP_009122816.1 274 FMKNKSKLISMLDEVYKRYKQYYEQLQAVMGSFECVAGLGHAAPYASLTLKALSRHFKCLKNAITEQL 341
                     5678**************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005742.4E-63212339IPR006563POX domain
PfamPF075261.9E-34217338IPR006563POX domain
SMARTSM003894.0E-9396460IPR001356Homeobox domain
CDDcd000862.37E-11396457No hitNo description
SuperFamilySSF466891.03E-16398463IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.608.1E-27400460IPR009057Homeodomain-like
PfamPF059202.0E-18413452IPR008422Homeobox KN domain
PROSITE profilePS5007111.645415456IPR001356Homeobox domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010051Biological Processxylem and phloem pattern formation
GO:0010076Biological Processmaintenance of floral meristem identity
GO:0010077Biological Processmaintenance of inflorescence meristem identity
GO:0010089Biological Processxylem development
GO:0010154Biological Processfruit development
GO:0010223Biological Processsecondary shoot formation
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048457Biological Processfloral whorl morphogenesis
GO:0048645Biological Processorgan formation
GO:0080006Biological Processinternode patterning
GO:0005634Cellular Componentnucleus
GO:0005829Cellular Componentcytosol
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 633 aa     Download sequence    Send to blast
MVLRKESKRS LSLSLNLLLS FHCHTIISST VTSLSLFFFC ISKSSLSMAD AYEPYHVLQQ  60
SRRDKLRIPS LDSHFHFHHP HPPSSSGGGA GVYPLGDSDY LAAGGFHSNN NSHISNPSYS  120
NFMGFLGGPS SSSSNAVAVA GDHSFHDGLS SGDVLVFKPE PLSLSLSSHP RLTYDLVVPG  180
VVNSGYGRSA AEAAAATVTV ASRSSGPLGP FTGYASILKG SRFLKPAQIL LDEFCNVGHG  240
IYTDKNIDGD DSSLLFDPTV ESLCGASDSG GGEFMKNKSK LISMLDEVYK RYKQYYEQLQ  300
AVMGSFECVA GLGHAAPYAS LTLKALSRHF KCLKNAITEQ LQFSTNNKIQ QQQQSGHLMI  360
SENRTESMRF GGSDSSRGLC SAGQRHGFPD NHAPVWRPHR GLPERAVTVL RAWLFDHFLH  420
PYPTDTDKLM LAKQTGLSRN QVSNWFINAR VRVWKPMVEE IHMLETRQSQ RSSSSSWRDE  480
RNTTTVFPDN NNNPSSSTAQ QRANNNSSPA RRVQNDDVHG TTTNNNNSNF MNAGNSGSGG  540
AVAFSYGIAS SNVAGMSSST NGGVSLTLGL HHQIGLPEPF PMTTAQRFGL EGGSSGGGGE  600
SYGGGGGYEV QNRQFGRDFI GGSNPQFLHD FVG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5bng_A7e-17402460159Homeobox protein Meis2
5bng_B7e-17402460159Homeobox protein Meis2
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed during late heart stage embryo in the SAM region between the two developing cotyledons. Expression is initially down-regulated in incipient floral primordia but a strong expression is subsequently detected in the central region of young floral primordia and the inner whorl of developing flowers. In fruit, is expressed in the replum of developing ovaries. {ECO:0000269|PubMed:12874117}.
UniprotTISSUE SPECIFICITY: Predominantly expressed in stems, inflorescences and flowers. {ECO:0000269|PubMed:12874117, ECO:0000269|PubMed:12897247, ECO:0000269|PubMed:13678595, ECO:0000269|PubMed:15019989}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that is involved in the preservation of the spiral phyllotactic arrangement leading to a regular pattern of organ initiation. Required for maintenance of stem cell fate in the shoot apical meristem, and is essential for specifying floral primordia and establishing early internode patterning events during inflorescence development. Acts as transcription repressor of AG expression in floral and inflorescence meristems. Is also responsive of the nuclear import of SHOOT MERISTEMLESS (STM). In the fruit, plays a central role in patterning by negatively regulating SHP expression in order to prevent replum cells from adopting a valve margin cell fate. {ECO:0000269|PubMed:12874117, ECO:0000269|PubMed:12897247, ECO:0000269|PubMed:13678595, ECO:0000269|PubMed:15019989, ECO:0000269|PubMed:15120075, ECO:0000269|PubMed:15155890, ECO:0000269|PubMed:16741748}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009122816.1
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_009122816.10.0PREDICTED: BEL1-like homeodomain protein 9
SwissprotQ9LZM80.0BLH9_ARATH; BEL1-like homeodomain protein 9
TrEMBLA0A397XPG90.0A0A397XPG9_BRACM; Uncharacterized protein
TrEMBLM4CZH10.0M4CZH1_BRARP; Uncharacterized protein
STRINGBra009618.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM56882746
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G02030.10.0TALE family protein
Publications ? help Back to Top
  1. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  2. Pabón-Mora N,Wong GK,Ambrose BA
    Evolution of fruit development genes in flowering plants.
    Front Plant Sci, 2014. 5: p. 300
    [PMID:25018763]
  3. Khan M, et al.
    Repression of Lateral Organ Boundary Genes by PENNYWISE and POUND-FOOLISH Is Essential for Meristem Maintenance and Flowering in Arabidopsis.
    Plant Physiol., 2015. 169(3): p. 2166-86
    [PMID:26417006]
  4. Andrés F, et al.
    Floral Induction in Arabidopsis by FLOWERING LOCUS T Requires Direct Repression of BLADE-ON-PETIOLE Genes by the Homeodomain Protein PENNYWISE.
    Plant Physiol., 2015. 169(3): p. 2187-99
    [PMID:26417007]
  5. Bencivenga S,Serrano-Mislata A,Bush M,Fox S,Sablowski R
    Control of Oriented Tissue Growth through Repression of Organ Boundary Genes Promotes Stem Morphogenesis.
    Dev. Cell, 2016. 39(2): p. 198-208
    [PMID:27666746]
  6. Sehra B,Franks RG
    Redundant CArG Box Cis-motif Activity Mediates SHATTERPROOF2 Transcriptional Regulation during Arabidopsis thaliana Gynoecium Development.
    Front Plant Sci, 2017. 8: p. 1712
    [PMID:29085379]
  7. Simonini S,Stephenson P,Østergaard L
    A molecular framework controlling style morphology in Brassicaceae.
    Development, 2018.
    [PMID:29440299]