IS3
- Family IS3
- Group IS3
Isoform Synonym(s)
Accession number | Transposition | Origin | Host |
---|---|---|---|
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 flank | Direct repeat | Right flank | DR Length |
---|---|---|---|
TAAATAAGTA | TAT | CACTTAAATA | 3 |
NNNNNAAGTA | TAT | CANNNNNNNN | 3 |
NNNTCATGAC | ATT | AACCTATAAN | 3 |
TGGTGAACAC | ACC | GACTACAACG | 3 |
AGGTGTGGCT | GTC | GTCATCATCA | 3 |
GATGACCGAG | ATC | CTGCACGATC | 3 |
ACAGGTTGTA | ATC | AGCCCCCCAC | 3 |
CCGTTCAGAA | AGC | TGATCTTACC | 3 |
NNNATAGTAA | ATG | TGCCCCCTAA | 3 |
CCGCTTCATA | CAT | CTCGTAGATT | 3 |
GGGATAAGCC | AAG | TTCATTTTTC | 3 |
CCTTTGGTAA | AGG | TTCTAAGCTC | 3 |
CTCAGGTGAG | AAC | ATCCCTGCCT | 3 |
TGCATGGGAT | CAT | TGGGTACTGT | 3 |
TCATTGGGTA | CTG | TGGGTTTNNN | 3 |
CAACGGAACA | ACT | CTCATTGCAT | 3 |
TGCATGGGAT | CATT | GGGTACTGTG | 4 |
CCCCACAACG | GAAC | AACTCTCATT | 4 |
DNA sequence
TGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCG
TAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCTGAAGCTTGCTGAACGCATCGGTGTTACTGCCGCAGCCCGTGAACTCAGCCTGTATGAATCACAA
CTCTACAACTGGCGCAGTAAACAGCAAAATCAGCAGACGTCTTCTGAACGTGAACTGGAGATGTCTACCGAGATTGCACGTCTCAAACGCCAGCTGGCAG
AACGGGATGAAGAGCTGGCTATCCTCCAAAAGGCCGCGACATACTTCGCGAAGCGCCTGAAATGAAGTATGTCTTTATTGAAAAACATCAGGCTGAGTTC
AGCATCAAAGCAATGTGCCGCGTGCTCCGGGTGGCCCGCAGCGGCTGGTATACGTGGTGTCAGCGGCGGACAAGGATAAGCACGCGTCAGCAGTTCCGCC
AACACTGCGACAGCGTTGTCCTCGCGGCTTTTACCCGGTCAAAACAGCGTTACGGTGCCCCACGCCTGACGGATGAACTGCGTGCTCAGGGTTACCCCTT
TAACGTAAAAACCGTGGCGGCAAGCCTGCGCCGTCAGGGACTGAGGGCAAAGGCCTCCCGGAAGTTCAGCCCGGTCAGCTACCGCGCACACGGCCTGCCT
GTGTCAGAAAATCTGTTGGAGCAGGATTTTTACGCCAGTGGCCCGAACCAGAAGTGGGCAGGAGACATCACGTACTTACGTACAGATGAAGGCTGGCTGT
ATCTGGCAGTGGTCATTGACCTGTGGTCACGTGCCGTTATTGGCTGGTCAATGTCGCCACGCATGACGGCGCAACTGGCCTGCGATGCCCTGCAGATGGC
GCTGTGGCGGCGTAAGAGGCCCCGGAACGTTATCGTTCACACGGACCGTGGAGGCCAGTACTGTTCAGCAGATTATCAGGCGCAACTGAAGCGGCATAAT
CTGCGTGGAAGTATGAGCGCAAAAGGTTGCTGCTACGATAATGCCTGCGTGGAAAGCTTCTTTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACT
TTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGA
ACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCA
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
Length | Begin | End | Strand | Fusion ORF | |
---|---|---|---|---|---|
300 bp | 99 aa | 66 | 365 | + | No |
Description : First part of the transposase
ORF sequence :
MTKTVSTSKKPRKQHSPEFRSEALKLAERIGVTAAARELSLYESQLYNWRSKQQNQQTSSERELEMSTEIARLKRQLAERDEELAILQKAATYFAKRLK
Blast result :ORF 2
Length | Begin | End | Strand | Fusion ORF | |
---|---|---|---|---|---|
918 bp | 305 aa | 311 | 1228 | + | No |
Description : Second part of the transposase
ORF sequence :
RAGYPPKGRDILREAPEMKYVFIEKHQAEFSIKAMCRVLRVARSGWYTWCQRRTRISTRQQFRQHCDSVVLAAFTRSKQRYGAPRLTDELRAQGYPFNVK
TVAASLRRQGLRAKASRKFSPVSYRAHGLPVSENLLEQDFYASGPNQKWAGDITYLRTDEGWLYLAVVIDLWSRAVIGWSMSPRMTAQLACDALQMALWR
RKRPRNVIVHTDRGGQYCSADYQAQLKRHNLRGSMSAKGCCYDNACVESFFHSLKVECIHGEHFISREIMRATVFNYIECDYNRWRRHSWCGGLSPEQFE
NKNLA
TVAASLRRQGLRAKASRKFSPVSYRAHGLPVSENLLEQDFYASGPNQKWAGDITYLRTDEGWLYLAVVIDLWSRAVIGWSMSPRMTAQLACDALQMALWR
RKRPRNVIVHTDRGGQYCSADYQAQLKRHNLRGSMSAKGCCYDNACVESFFHSLKVECIHGEHFISREIMRATVFNYIECDYNRWRRHSWCGGLSPEQFE
NKNLA
Blast result :ORF 3
Length | Begin | End | Strand | Fusion ORF | |
---|---|---|---|---|---|
1163 bp | 387 aa | 66 | 1228 | + | Yes |
Chemistry : DDE
ORF sequence :
MTKTVSTSKKPRKQHSPEFRSEALKLAERIGVTAAARELSLYESQLYNWRSKQQNQQTSSERELEMSTEIARLKRQLAERDEELAILQKGRDILREAPEM
KYVFIEKHQAEFSIKAMCRVLRVARSGWYTWCQRRTRISTRQQFRQHCDSVVLAAFTRSKQRYGAPRLTDELRAQGYPFNVKTVAASLRRQGLRAKASRK
FSPVSYRAHGLPVSENLLEQDFYASGPNQKWAGDITYLRTDEGWLYLAVVIDLWSRAVIGWSMSPRMTAQLACDALQMALWRRKRPRNVIVHTDRGGQYC
SADYQAQLKRHNLRGSMSAKGCCYDNACVESFFHSLKVECIHGEHFISREIMRATVFNYIECDYNRWRRHSWCGGLSPEQFENKNLA
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