ISShfr6
- Family IS3
- Group IS3
Isoform Synonym(s)
| Accession number | Transposition | Origin | Host |
|---|---|---|---|
| NC_008345 | ND | Shewanella frigidimarina | Shewanella frigidimarina NCBM4000 |
DNA section
IS Length : 1260 bp
Ends
IR Length : 26/36
IRL : TGTAGTGGCATAGTTATTTTGGCCACCTAAATAGAGGTGATATTATTACC
IRR : TGTAGTGGTCAAGTAATATTGGCCACGGTTTTAGAGTCATTCCAATATAA
Insertion site
| Left flank | Direct repeat | Right flank | DR Length |
|---|---|---|---|
| CACTACTCTA | GAT | GCTGAAATAG | 3 |
| ACAGAGGTGT | GGAT | AGTGTGGTGT | 4 |
| ATCCATGTGC | CTC | AAGGCATTCC | 3 |
| TTATGCTCAT | GTA | TGAATAGATG | 3 |
| TTGACTCTCG | CAT | ATACCTCTTC | 3 |
| TTTATACATTG | GTGCGTTATTT | 0 | |
| AATAGAGTCC | CTC | GTTGATAGAG | 3 |
| GTAAATAATT | AAC | TGACTCTATA | 3 |
| AGCTAACCAC | ATATCATTTC | 0 |
DNA sequence
TGTAGTGGCATAGTTATTTTGGCCACCTAAATAGAGGTGATATTATTACCTCGTACATGACTTTAGGTGAACACATGAGATCGATAACCAGAAAAACATT
TAGTGCTGAATTCAAACTTGAAGCAGCCCAATTAGTCCTCGATAAAAACCATAGCATCATCGAAGCAGCAAAGGCGATGAACGTGGGTAAATCAACCATG
GATAAATGGGTGAGACAGTTAAAACTAGAACGCCAGGGTGGCACGCCAAAAGCCTCTCCCATTACCCCTGAACAAATTGAAATCCGTGAACTGAAGAAAC
AGGTAGCCCGTCTTGAGGAGCATAATCTTATTCTAAAAAAGGCTACCGCTCTCTTGATGTCAGACTCGATGAACAATTTACGCTGATCAGCGCACTCAAG
CAGAGCCACTCTATTCTCACAATTTGTAATGCATTCAAAGTGCATCGAAGTAGCTATAAATATTGGCTAAAAAGAAAAGAACATATCGATGCTGACTTTA
CTATTTTATGCAGTGAAGTGAAGGCCGCGCATCGTATTAGTAATGGCTCTGCCGGTGCTAGAACGATAGCGCAATTAGTGACTAACAAAGGGATTAATCT
CAGTCGTTATCGAGCCCGTAATCTAATGAGAAAGCTTGGATTATTAAGCTGTCAGCAGCCTAAGCATTCTTATAGGAAAGCTGCACAAGAGCATGTAGCG
ATCCCAAACACGCTTAATCGACAGTTTGCAGTAACTCAACCAGATCAAGTGTGGTGTGGCGATGTGACGTATGTTTGGGTCGGTAATCGTTGGGCATATT
TAGCCGTTGTTTTAGACTTATTTTCCCGCAAACCTGTTGGGTGGGCTTTGTCATTATCGCCTGACAGCGAGCTGACCTCTAAAGCCTTGAAAATGGCATT
TGAGTTAAGGGGGAAACCTGAGAATGTGATATATCACAGCGACCAAGGTTCACATTACACAAGCTTGAAATTCAGACAGTTATTATGGCGTCTTCAGATT
GAGCAAAGCATGAGTCGTCGCGGGAATTGTTGGGATAACGCACCAATGGAGCGTTTCTTTAGAAGTTTGAAATCTGAATGGGTACCCGCAAGTGGCTATG
GGAATTTTACAGAAGCAGACAAAGCGATCACAAATTACATCACTGGATATTACAGTGAAACTAGACCCCATCAATATAATGGTGGGTTAACTCCAAATGA
GTCAGAACGTTTATATTGGAATGACTCTAAAACCGTGGCCAATATTACTTGACCACTACA
TAGTGCTGAATTCAAACTTGAAGCAGCCCAATTAGTCCTCGATAAAAACCATAGCATCATCGAAGCAGCAAAGGCGATGAACGTGGGTAAATCAACCATG
GATAAATGGGTGAGACAGTTAAAACTAGAACGCCAGGGTGGCACGCCAAAAGCCTCTCCCATTACCCCTGAACAAATTGAAATCCGTGAACTGAAGAAAC
AGGTAGCCCGTCTTGAGGAGCATAATCTTATTCTAAAAAAGGCTACCGCTCTCTTGATGTCAGACTCGATGAACAATTTACGCTGATCAGCGCACTCAAG
CAGAGCCACTCTATTCTCACAATTTGTAATGCATTCAAAGTGCATCGAAGTAGCTATAAATATTGGCTAAAAAGAAAAGAACATATCGATGCTGACTTTA
CTATTTTATGCAGTGAAGTGAAGGCCGCGCATCGTATTAGTAATGGCTCTGCCGGTGCTAGAACGATAGCGCAATTAGTGACTAACAAAGGGATTAATCT
CAGTCGTTATCGAGCCCGTAATCTAATGAGAAAGCTTGGATTATTAAGCTGTCAGCAGCCTAAGCATTCTTATAGGAAAGCTGCACAAGAGCATGTAGCG
ATCCCAAACACGCTTAATCGACAGTTTGCAGTAACTCAACCAGATCAAGTGTGGTGTGGCGATGTGACGTATGTTTGGGTCGGTAATCGTTGGGCATATT
TAGCCGTTGTTTTAGACTTATTTTCCCGCAAACCTGTTGGGTGGGCTTTGTCATTATCGCCTGACAGCGAGCTGACCTCTAAAGCCTTGAAAATGGCATT
TGAGTTAAGGGGGAAACCTGAGAATGTGATATATCACAGCGACCAAGGTTCACATTACACAAGCTTGAAATTCAGACAGTTATTATGGCGTCTTCAGATT
GAGCAAAGCATGAGTCGTCGCGGGAATTGTTGGGATAACGCACCAATGGAGCGTTTCTTTAGAAGTTTGAAATCTGAATGGGTACCCGCAAGTGGCTATG
GGAATTTTACAGAAGCAGACAAAGCGATCACAAATTACATCACTGGATATTACAGTGAAACTAGACCCCATCAATATAATGGTGGGTTAACTCCAAATGA
GTCAGAACGTTTATATTGGAATGACTCTAAAACCGTGGCCAATATTACTTGACCACTACA
Recoding section
- Recoding by frameshift
- Frame
- Type
- Experimentally demonstrated
Stimulators :
- Shine-Dalgarno sequence :
- Secondary structure :
Recoding motif :
Protein section
ORF number : 3
ORF 1
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 312 bp | 103 aa | 75 | 386 | + | No |
Description : First part of the transposase
ORF sequence :
MRSITRKTFSAEFKLEAAQLVLDKNHSIIEAAKAMNVGKSTMDKWVRQLKLERQGGTPKASPITPEQIEIRELKKQVARLEEHNLILKKATALLMSDSMN
NLR
NLR
Blast result :ORF 2
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 866 bp | 303 aa | 387 | 1252 | + | No |
Description : Second part of the transposase
ORF sequence :
GYRSLDVRLDEQFTLISALKQSHSILTICNAFKVHRSSYKYWLKRKEHIDADFTILCSEVKAAHRISNGSAGARTIAQLVTNKGINLSRYRARNLMRKLG
LLSCQQPKHSYRKAAQEHVAIPNTLNRQFAVTQPDQVWCGDVTYVWVGNRWAYLAVVLDLFSRKPVGWALSLSPDSELTSKALKMAFELRGKPENVIYHS
DQGSHYTSLKFRQLLWRLQIEQSMSRRGNCWDNAPMERFFRSLKSEWVPASGYGNFTEADKAITNYITGYYSETRPHQYNGGLTPNESERLYWNDSKTVA
NIT
LLSCQQPKHSYRKAAQEHVAIPNTLNRQFAVTQPDQVWCGDVTYVWVGNRWAYLAVVLDLFSRKPVGWALSLSPDSELTSKALKMAFELRGKPENVIYHS
DQGSHYTSLKFRQLLWRLQIEQSMSRRGNCWDNAPMERFFRSLKSEWVPASGYGNFTEADKAITNYITGYYSETRPHQYNGGLTPNESERLYWNDSKTVA
NIT
Blast result :ORF 3
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1178 bp | 392 aa | 75 | 1252 | + | Yes |
Chemistry : DDE
ORF sequence :
MRSITRKTFSAEFKLEAAQLVLDKNHSIIEAAKAMNVGKSTMDKWVRQLKLERQGGTPKASPITPEQIEIRELKKQVARLEEHNLILKKGYRSLDVRLDE
QFTLISALKQSHSILTICNAFKVHRSSYKYWLKRKEHIDADFTILCSEVKAAHRISNGSAGARTIAQLVTNKGINLSRYRARNLMRKLGLLSCQQPKHSY
RKAAQEHVAIPNTLNRQFAVTQPDQVWCGDVTYVWVGNRWAYLAVVLDLFSRKPVGWALSLSPDSELTSKALKMAFELRGKPENVIYHSDQGSHYTSLKF
RQLLWRLQIEQSMSRRGNCWDNAPMERFFRSLKSEWVPASGYGNFTEADKAITNYITGYYSETRPHQYNGGLTPNESERLYWNDSKTVANIT
QFTLISALKQSHSILTICNAFKVHRSSYKYWLKRKEHIDADFTILCSEVKAAHRISNGSAGARTIAQLVTNKGINLSRYRARNLMRKLGLLSCQQPKHSY
RKAAQEHVAIPNTLNRQFAVTQPDQVWCGDVTYVWVGNRWAYLAVVLDLFSRKPVGWALSLSPDSELTSKALKMAFELRGKPENVIYHSDQGSHYTSLKF
RQLLWRLQIEQSMSRRGNCWDNAPMERFFRSLKSEWVPASGYGNFTEADKAITNYITGYYSETRPHQYNGGLTPNESERLYWNDSKTVANIT
Blast result :
Comments
There are 9 copies of ISShfr6 encoded in the Shewanella frigidimarina chromosome. Orf1 and Orf2 are predicted to undergo a programmed frameshift to produce Orf3. The ISShfr6 transposase has 97% identity with ISSba5.
References
1] Romine, M. F. (2008) Direct submission.