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 Rsa1.0_00129.1_g00029.1
Organism
Raphanus sativus
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: 579aa    MW: 62642.4 Da    PI: 7.4525
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_00129.1_g00029.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox283.6e-093684002254
                              SSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHH CS
                 Homeobox  22 nrypsaeereeLAkklgLterqVkvWFqNrRak 54 
                              ++yp+ +++  LAk++gL+ +qV++WF N R +
  Rsa1.0_00129.1_g00029.1 368 HPYPTDTDKLMLAKQTGLSRNQVSNWFINARVR 400
                              89*****************************87 PP
2BELL106.51.7e-34223290572
                     BELL   5 lqkkkakLlslleeVdkrYkqyveqlqtvissFeavaglgsakpYtslAlkaiSrhFrcLkdaiaeqi 72 
                                k k+kL+s+l+eV+krYkqy+eqlq+v++sFe+vaglg+a+pY+s+ lka+SrhF+cLk+ai+eq+
  Rsa1.0_00129.1_g00029.1 223 YMKNKSKLISMLDEVYKRYKQYYEQLQAVMGSFECVAGLGHAAPYASFTLKALSRHFKCLKNAITEQL 290
                              56789*************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005744.2E-60165288IPR006563POX domain
PfamPF075264.4E-34170287IPR006563POX domain
CDDcd000862.04E-11344405No hitNo description
SMARTSM003894.0E-9344408IPR001356Homeobox domain
SuperFamilySSF466897.27E-17346412IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.607.2E-27348408IPR009057Homeodomain-like
PfamPF059201.8E-18361400IPR008422Homeobox KN domain
PROSITE profilePS5007111.645363404IPR001356Homeobox 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: 579 aa     Download sequence    Send to blast
MADAYEPYHV LQQSRRDKLR IPSLDSHFHF HHPHPPSSSG VGVGVYPLSD SDYLAPGGFH  60
SNNNSHISNP SYSNFMGFLG GPSSSSSNAV AVAGDHSFHD GLSSGDVLVF KPEPLSLSLS  120
SHPRLTYDLV VPGVVNSGFS RSAAEAAAAA VTVASRSSGP LGPFTGYASI LKGSRFLKPA  180
QILLDEFCNV GHGIYTDKNI DGDDSSMLFD PTVESLCGGG GEYMKNKSKL ISMLDEVYKR  240
YKQYYEQLQA VMGSFECVAG LGHAAPYASF TLKALSRHFK CLKNAITEQL QFSTNNKIQQ  300
QQSGHLMITE NRTESMRFGG SDSSRGLCSA GQRHGFPDNH APVWRPHRGL PERAVTVLRA  360
WLFDHFLHPY PTDTDKLMLA KQTGLSRNQV SNWFINARVR VWKPMVEEIH MLETRQSQRP  420
SSSSWRDERN TTAVLPDNNN PSSSPAQQRA NNNSSPARRV QNDDVHGTTT NNNNNFMNAG  480
NSGSGGAVGF SYGIASSNVA GMSSSTNGGV SLTLGLHHQI GLPEPFPMTT AQRFGLDGGS  540
SGGGGESYGG GGEYEVQNRQ FGRDFIGGSN PQFLHDFVG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4xrs_A1e-16350407158Homeobox protein Meis1
4xrs_B1e-16350407158Homeobox protein Meis1
5bng_A1e-16350408159Homeobox protein Meis2
5bng_B1e-16350408159Homeobox 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_00129.1_g00029.1
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
TrEMBLA0A078FED50.0A0A078FED5_BRANA; BnaCnng03740D 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]