IS3

  • Family IS3
  • Group IS3
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
X02311 Y Escherichia coli
Escherichia coli W3110
Salmonella typhimurium SARA17
Escherichia coli K-12
Escherichia coli B
Escherichia coli BHB2600
Escherichia coli HB101
Salmonella dysenteriae
Salmonella flexneri
Salmonella heidelberg SARA30
Salmonella muenchen SARA64
Salmonella odorifera
Salmonella paratyphi SARA41
Salmonella saintpaul SARA24
Salmonella typhimurium SARA7
Salmonella typhimurium SARA13
DNA section
IS Length : 1258 bp

Ends


IR Length : 29/40

IRL : TGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAG
IRR : TGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTT

Insertion site


Left flankDirect repeatRight flankDR Length
TAAATAAGTATATCACTTAAATA3
NNNNNAAGTATATCANNNNNNNN3
NNNTCATGACATTAACCTATAAN3
TGGTGAACACACCGACTACAACG3
AGGTGTGGCTGTCGTCATCATCA3
GATGACCGAGATCCTGCACGATC3
ACAGGTTGTAATCAGCCCCCCAC3
CCGTTCAGAAAGCTGATCTTACC3
NNNATAGTAAATGTGCCCCCTAA3
CCGCTTCATACATCTCGTAGATT3
GGGATAAGCCAAGTTCATTTTTC3
CCTTTGGTAAAGGTTCTAAGCTC3
CTCAGGTGAGAACATCCCTGCCT3
TGCATGGGATCATTGGGTACTGT3
TCATTGGGTACTGTGGGTTTNNN3
CAACGGAACAACTCTCATTGCAT3
TGCATGGGATCATTGGGTACTGTG4
CCCCACAACGGAACAACTCTCATT4

DNA sequence

TGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCG
TAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCTGAAGCTTGCTGAACGCATCGGTGTTACTGCCGCAGCCCGTGAACTCAGCCTGTATGAATCACAA
CTCTACAACTGGCGCAGTAAACAGCAAAATCAGCAGACGTCTTCTGAACGTGAACTGGAGATGTCTACCGAGATTGCACGTCTCAAACGCCAGCTGGCAG
AACGGGATGAAGAGCTGGCTATCCTCCAAAAGGCCGCGACATACTTCGCGAAGCGCCTGAAATGAAGTATGTCTTTATTGAAAAACATCAGGCTGAGTTC
AGCATCAAAGCAATGTGCCGCGTGCTCCGGGTGGCCCGCAGCGGCTGGTATACGTGGTGTCAGCGGCGGACAAGGATAAGCACGCGTCAGCAGTTCCGCC
AACACTGCGACAGCGTTGTCCTCGCGGCTTTTACCCGGTCAAAACAGCGTTACGGTGCCCCACGCCTGACGGATGAACTGCGTGCTCAGGGTTACCCCTT
TAACGTAAAAACCGTGGCGGCAAGCCTGCGCCGTCAGGGACTGAGGGCAAAGGCCTCCCGGAAGTTCAGCCCGGTCAGCTACCGCGCACACGGCCTGCCT
GTGTCAGAAAATCTGTTGGAGCAGGATTTTTACGCCAGTGGCCCGAACCAGAAGTGGGCAGGAGACATCACGTACTTACGTACAGATGAAGGCTGGCTGT
ATCTGGCAGTGGTCATTGACCTGTGGTCACGTGCCGTTATTGGCTGGTCAATGTCGCCACGCATGACGGCGCAACTGGCCTGCGATGCCCTGCAGATGGC
GCTGTGGCGGCGTAAGAGGCCCCGGAACGTTATCGTTCACACGGACCGTGGAGGCCAGTACTGTTCAGCAGATTATCAGGCGCAACTGAAGCGGCATAAT
CTGCGTGGAAGTATGAGCGCAAAAGGTTGCTGCTACGATAATGCCTGCGTGGAAAGCTTCTTTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACT
TTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGA
ACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCA
Recoding section
  • Recoding by frameshift
  • Frame -1
  • Type translational
  • Experimentally demonstrated Yes

Stimulators :

  • Shine-Dalgarno sequence : Yes
  • Secondary structure : pseudoknot

Recoding motif :

UGAAGAGCUGGCUAUCCUCCAAAAGGCCGCGACAUACUUCGCGAAGCGCC
..............................(((((((((((......[[[
UGAAAUGAAGUAUGUCUUUAUUGAAAAACAUCAGGCUGAGUUCAGCAUCA
[[[..)))))))))))..............]]]]]]
AAGCAAUGUGCCGCGUGCUCCGGGUGGCCCGCA
Protein section
ORF number : 3

 

ORF 1
LengthBeginEndStrandFusion ORF
300 bp99 aa66365+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MTKTVSTSKKPRKQHSPEFRSEALKLAERIGVTAAARELSLYESQLYNWRSKQQNQQTSSERELEMSTEIARLKRQLAERDEELAILQKAATYFAKRLK

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
918 bp305 aa3111228+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

RAGYPPKGRDILREAPEMKYVFIEKHQAEFSIKAMCRVLRVARSGWYTWCQRRTRISTRQQFRQHCDSVVLAAFTRSKQRYGAPRLTDELRAQGYPFNVK
TVAASLRRQGLRAKASRKFSPVSYRAHGLPVSENLLEQDFYASGPNQKWAGDITYLRTDEGWLYLAVVIDLWSRAVIGWSMSPRMTAQLACDALQMALWR
RKRPRNVIVHTDRGGQYCSADYQAQLKRHNLRGSMSAKGCCYDNACVESFFHSLKVECIHGEHFISREIMRATVFNYIECDYNRWRRHSWCGGLSPEQFE
NKNLA

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
1163 bp387 aa661228+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MTKTVSTSKKPRKQHSPEFRSEALKLAERIGVTAAARELSLYESQLYNWRSKQQNQQTSSERELEMSTEIARLKRQLAERDEELAILQKGRDILREAPEM
KYVFIEKHQAEFSIKAMCRVLRVARSGWYTWCQRRTRISTRQQFRQHCDSVVLAAFTRSKQRYGAPRLTDELRAQGYPFNVKTVAASLRRQGLRAKASRK
FSPVSYRAHGLPVSENLLEQDFYASGPNQKWAGDITYLRTDEGWLYLAVVIDLWSRAVIGWSMSPRMTAQLACDALQMALWRRKRPRNVIVHTDRGGQYC
SADYQAQLKRHNLRGSMSAKGCCYDNACVESFFHSLKVECIHGEHFISREIMRATVFNYIECDYNRWRRHSWCGGLSPEQFENKNLA

 

Blast result :
Comments
There are seven IS3 copies in the chromosome of Escherichia coli BHB2600. IS3 is more prevalent in the Salmonella typhimurium SARA strains than IS200 (Bisercic and Ochman, 1993). Homologous recombination between chromosomal and/or extrachromosomal copies of IS3 have been largely documented, including their involvement in F integration (Deonier and Hadley, 1980) or large chromosomal DNA inversion (Savic et al., 1983, Ajdic et al., 1991, Komoda et al., 1991). The observation of 4-bp DR formulated by Sommer et al. (1979) corresponded to a misinterpretetion of IS3 ends. However, 4-bp DR have been observed in 2/20 cases (Spielmann-Ryser et al., 1991). IS3 transposition has been shown to "turn-on" chromosomal genes and this element can be considered as a mobile promoter (Zafarullah et al., 1981, Charlier et al., 1982). Three proteins are encoded by IS3: OrfA, OrfB (unknown function) and the transframe protein OrfAB (the actual transposase). Minicircles, consisting of the entire IS3 sequence and three bp between the IS3 ends have been observed in vivo (Sekine et al., 1994).
References