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 RrC915_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: 325aa    MW: 36939.3 Da    PI: 4.6089
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC915_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox29.41.3e-092683022155
                HSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHH CS
   Homeobox  21 knrypsaeereeLAkklgLterqVkvWFqNrRake 55 
                k +yp+++++  LA+++gL+++q+ +WF N+R ++
  RrC915_p1 268 KWPYPTEADKIALAEETGLDQKQINNWFINQRKRH 302
                569*****************************885 PP
2ELK34.64e-12222243122
        ELK   1 ELKhqLlrKYsgyLgsLkqEFs 22 
                ELK+qLlrK++++++sLk EFs
  RrC915_p1 222 ELKDQLLRKFGSHISSLKLEFS 243
                9********************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM012558.0E-2081125IPR005540KNOX1
PfamPF037909.4E-2083124IPR005540KNOX1
SMARTSM012567.7E-27132183IPR005541KNOX2
PfamPF037913.7E-25136182IPR005541KNOX2
PROSITE profilePS5121310.109222242IPR005539ELK domain
PfamPF037894.0E-9222243IPR005539ELK domain
SMARTSM011881.1E-6222243IPR005539ELK domain
PROSITE profilePS5007112.876242305IPR001356Homeobox domain
SuperFamilySSF466898.98E-20243315IPR009057Homeodomain-like
SMARTSM003898.1E-14244309IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.607.5E-28247306IPR009057Homeodomain-like
CDDcd000865.04E-13251306No hitNo description
PfamPF059207.6E-18262301IPR008422Homeobox KN domain
PROSITE patternPS000270280303IPR017970Homeobox, conserved site
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009723Biological Processresponse to ethylene
GO:0009736Biological Processcytokinin-activated signaling pathway
GO:0010094Biological Processspecification of carpel identity
GO:0005634Cellular Componentnucleus
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 325 aa     Download sequence    Send to blast
MDRMCGFRSA GDYQEKAAVV MSSSESLMSL SDYQNFICSS AGENYVFGSD ELFSAATAAS  60
VLSSEAVSIA PRVRRADQDN NFIKSKIASH PLYPRLLQTY IDCQKVGAPF EIACVLEEIQ  120
RENDVYKRDV APLSCYGADP ELDEFMETYC DILVKYKSDL ARPFDEATTF LNKIETQLQD  180
LCTGPASARG LSDDGAVSSD EELREGDDVA TQDSQQRSND RELKDQLLRK FGSHISSLKL  240
EFSKKKKKGK LPREARQALL DWWNVHYKWP YPTEADKIAL AEETGLDQKQ INNWFINQRK  300
RHWKPSENMP FAMMDDSSET FFTEE
Functional Description ? help Back to Top
Source Description
UniProtMay play a role in meristem function, and may be involved in maintaining cells in an undifferentiated, meristematic state. Probably binds to the DNA sequence 5'-TGAC-3'.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankX813530.0X81353.1 A.thaliana mRNA for ATK1 protein.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018471943.10.0PREDICTED: homeobox protein knotted-1-like 2 isoform X1
SwissprotP466400.0KNAT2_ARATH; Homeobox protein knotted-1-like 2
TrEMBLA0A398AAQ30.0A0A398AAQ3_BRACM; Uncharacterized protein
TrEMBLM4CUM50.0M4CUM5_BRARP; Uncharacterized protein
STRINGBra007920.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM8352785
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G70510.11e-178KNOTTED-like from Arabidopsis thaliana 2
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. Zhang XL,Yang ZP,Zhang J,Zhang LG
    Ectopic expression of BraYAB1-702, a member of YABBY gene family in Chinese cabbage, causes leaf curling, inhibition of development of shoot apical meristem and flowering stage delaying in Arabidopsis thaliana.
    Int J Mol Sci, 2013. 14(7): p. 14872-91
    [PMID:23863694]
  3. Kuijt SJ, et al.
    Interaction between the GROWTH-REGULATING FACTOR and KNOTTED1-LIKE HOMEOBOX families of transcription factors.
    Plant Physiol., 2014. 164(4): p. 1952-66
    [PMID:24532604]
  4. Scofield S,Dewitte W,Murray JA
    STM sustains stem cell function in the Arabidopsis shoot apical meristem and controls KNOX gene expression independently of the transcriptional repressor AS1.
    Plant Signal Behav, 2018.
    [PMID:24776954]
  5. Lee JE,Lampugnani ER,Bacic A,Golz JF
    SEUSS and SEUSS-LIKE 2 coordinate auxin distribution and KNOXI activity during embryogenesis.
    Plant J., 2014. 80(1): p. 122-35
    [PMID:25060324]
  6. Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y
    The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis.
    Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71
    [PMID:26108442]
  7. Li Z, et al.
    Transcription factors AS1 and AS2 interact with LHP1 to repress KNOX genes in Arabidopsis.
    J Integr Plant Biol, 2016. 58(12): p. 959-970
    [PMID:27273574]
  8. Lozano-Sotomayor P, et al.
    Altered expression of the bZIP transcription factor DRINK ME affects growth and reproductive development in Arabidopsis thaliana.
    Plant J., 2016. 88(3): p. 437-451
    [PMID:27402171]