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 RrC3966_p1
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family TALE
Protein Properties Length: 578aa    MW: 61839.4 Da    PI: 7.3718
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC3966_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox283.6e-093623942254
                 SSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHH CS
    Homeobox  22 nrypsaeereeLAkklgLterqVkvWFqNrRak 54 
                 ++yp+ +++  LAk++gL+ +qV++WF N R +
  RrC3966_p1 362 HPYPTDTDKLMLAKQTGLSRNQVSNWFINARVR 394
                 89*****************************87 PP
2BELL106.91.2e-34227295472
        BELL   4 elqkkkakLlslleeVdkrYkqyveqlqtvissFeavaglgsakpYtslAlkaiSrhFrcLkdaiaeqi 72 
                 e  kkk+kL+s+l+eV+krYkqy+eqlq+v++sFe+vaglg+a+pY+sl lk +S+hF+cLk+ai++q+
  RrC3966_p1 227 ESGKKKSKLISMLDEVYKRYKQYYEQLQAVMGSFECVAGLGHAAPYASLTLKVLSKHFKCLKNAITDQL 295
                 6679**************************************************************997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005741.6E-61164293IPR006563POX domain
PfamPF075264.1E-35169292IPR006563POX domain
CDDcd000862.03E-11338399No hitNo description
SMARTSM003894.0E-9338402IPR001356Homeobox domain
SuperFamilySSF466898.55E-17340405IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.607.2E-27342402IPR009057Homeodomain-like
PfamPF059201.8E-18355394IPR008422Homeobox KN domain
PROSITE profilePS5007111.645357398IPR001356Homeobox 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: 578 aa     Download sequence    Send to blast
MSDAYEPYHV LQQSRRDKLR IPSFDSHFHF HHPLPPPSSS GGGVFPTADS DFLAAGGFHS  60
NSNNNNPSYS NFMGFLGGPS SSSSTAVAVA GDHSFNAGLS SGDVLVFKPE PLSLSLSSHP  120
RPTYDLVVPG VVNSGFCRSA AEAAAAAAAV TVASRSSGPL GPFTGYASIL KGSKFLKPAQ  180
MLLDDFCSVS RAVYTEQNID DDEDDSSLLF DPTIDNLCGV SDAGLGESGK KKSKLISMLD  240
EVYKRYKQYY EQLQAVMGSF ECVAGLGHAA PYASLTLKVL SKHFKCLKNA ITDQLQFSTN  300
NKIQQQQQFL GFGGSDSSRG LCSAGQRHGF LDNHAPVWRP HRGLPERAVT VLRAWLFDHF  360
LHPYPTDTDK LMLAKQTGLS RNQVSNWFIN ARVRVWKPMV EEIHMLETRQ SQKSSSSWRD  420
TTTVFPDNNN NPSSSTAQQR ANNSSSPARR VRNEDVHATT NNNNNRFMNA GNGGNVGGGG  480
AVSFSYGIAS SNVPGMNTST NGGVSLTLGL HHQIGLPEPF PMTTAQRFGL DAGSSGGGGG  540
GGGGESYGGG GGYEGQDRSF GRDFIGGSNH QFLHDFVG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4xrm_A8e-17344402563Homeobox protein Meis2
4xrm_B8e-17344402563Homeobox protein Meis2
5bng_A7e-17344402159Homeobox protein Meis2
5bng_B7e-17344402159Homeobox protein Meis2
Search in ModeBase
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}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1896460.0AC189646.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrS009G14, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018447293.10.0PREDICTED: BEL1-like homeodomain protein 9
SwissprotQ9LZM80.0BLH9_ARATH; BEL1-like homeodomain protein 9
TrEMBLA0A398A4V30.0A0A398A4V3_BRACM; Uncharacterized protein
STRINGBra028883.1-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]