PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Rsa1.0_01689.1_g00002.1
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: 425aa    MW: 46255 Da    PI: 8.76
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_01689.1_g00002.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox28.62.5e-092212532254
                              SSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHH CS
                 Homeobox  22 nrypsaeereeLAkklgLterqVkvWFqNrRak 54 
                              ++yp+ +++  LAk++gL+ +qV++WF N R +
  Rsa1.0_01689.1_g00002.1 221 HPYPTDTDKLMLAKQTGLSRNQVSNWFINARVR 253
                              89*****************************87 PP
2BELL82.55.3e-271011551872
                     BELL  18 eVdkrYkqyveqlqtvissFeavaglgsakpYtslAlkaiSrhFrcLkdaiaeqi 72 
                               V+krYkqy+eqlq+v++sFe+vaglg+a+pY+sl lk +S+hF+cLk+ai++q+
  Rsa1.0_01689.1_g00002.1 101 DVYKRYKQYYEQLQAVMGSFECVAGLGHAAPYASLTLKVLSKHFKCLKNAITDQL 155
                              699*************************************************997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005742.7E-1341153IPR006563POX domain
PfamPF075264.0E-19102152IPR006563POX domain
CDDcd000861.41E-11197258No hitNo description
SMARTSM003894.0E-9197261IPR001356Homeobox domain
SuperFamilySSF466895.13E-17199264IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.604.6E-27201261IPR009057Homeodomain-like
PfamPF059201.2E-18214253IPR008422Homeobox KN domain
PROSITE profilePS5007111.645216257IPR001356Homeobox domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 425 aa     Download sequence    Send to blast
MSDAYEPYHV LQQSRRDKLR LPSLDSHFHF HHPLPPPPSS SGGVFPTADS DFLAAGGGFH  60
SNSNNNPSYS NFMGFLGGPS SSSSTAVAVD HSFNAGLSSG DVYKRYKQYY EQLQAVMGSF  120
ECVAGLGHAA PYASLTLKVL SKHFKCLKNA ITDQLQFSTN NKIQQQQFLE FGGNDSSRGL  180
CSAGQRHGFP DHHAPVWRPH RGLPERAVTV LRAWLFDHFL HPYPTDTDKL MLAKQTGLSR  240
NQVSNWFINA RVRVWKPMVE EIHMLETRQS QKSSSSWRDT TTVFPDHNNN PSSSTAQQAN  300
NSSSPARRVR NDDVHAITNN NNNRFMNAGN GGNVGGGGAV NFSYGIASSN VPGMNTSTNG  360
GVSLTLGLHH QIGLPEPFPM TTAQRFGLDA GSSGGGGGGY EGQDRSFGRD FIGGSNHQFL  420
HDFVG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4xrm_A3e-16203261563Homeobox protein Meis2
4xrm_B3e-16203261563Homeobox protein Meis2
4xrs_A3e-16203260158Homeobox protein Meis1
4xrs_B3e-16203260158Homeobox protein Meis1
5bng_A2e-16203261159Homeobox protein Meis2
5bng_B2e-16203261159Homeobox 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_01689.1_g00002.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
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
SwissprotQ9LZM81e-164BLH9_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
AT5G02030.11e-157TALE 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]