ISShfr4
- Family IS3
- Group IS3
Isoform Synonym(s)
| Accession number | Transposition | Origin | Host |
|---|---|---|---|
| NC_008345 | ND | Shewanella frigidimarina | Shewanella frigidimarina NCBM4000 |
DNA section
IS Length : 1302 bp
Ends
IR Length : 19/24
IRL : TGTCCCGTCCTGAGATAAGTTGACACATTGGAGACTTATCTATGAAACCT
IRR : TGTCTAGTCCTAAAATAGGTTGACGGTTTTTATTAAGCCAGTTGGAACTC
Insertion site
| Left flank | Direct repeat | Right flank | DR Length |
|---|---|---|---|
| TTTTATTTTA | ACA | CTGCGCACTA | 3 |
| TGGATTCTTG | AGC | TGATTTTACA | 3 |
| TTTCTTTTTT | AAG | TTGCTTGCAG | 3 |
DNA sequence
TGTCCCGTCCTGAGATAAGTTGACACATTGGAGACTTATCTATGAAACCTTCAGTATCAATCAATATAAAACGTACTCAACGAGATTACACGTTAGGCTT
TAAATTAGCGGTTGTTAGTCAAGTAGAAAAAGGCGAGCTAACGTATAAGCAAGCTCAAGACCATTATGGCATTCAAGGGAGAAGTACCGTCCTAACATGG
TTACGAAAACATGGTAGATTAGATTGGTCCCAGCCGATTGAGCATTCACCTATGTCCAAATCTACAGAAACACCCGCCCAGAAAATCAAACGATTAGAGA
AACAAGTCTCCAATCTCGAAATGAAAAATATGATTTATGGCGATATGGTCGAGTTACTTAAAAATGAGTACGGTATTGATTTAGAAAAAAAGTACTTAGC
CGAACGCTCTGGCTTGCCAAAGAAAAAGGCACTGTAAAGCTAGCGACAGCGAGTCGGCAGTTTAACCTATCAAGACAAGCTGTTTATCAATGGAAGCAGC
GCTTAGCAGCAAGAGCTGACATGTTAAAACCGGTGATGACGATGGTTATGTATTGGCGTCAGTTCATGCCCAGAGTGGGTACGCGTAAGCTTTATCAACT
CATCAAGCCACAGTTACTTAAACAAGGCATAAAGCTAGGTAGGGACGGCCTATTTCGGTATTTGAAACAACACAATATGTTAGTAAGGCCTAGGAAGAAT
TACACCAAGACAACCCATAGCCATCATTGGTTGAGAAAACACCCAAACTTACTCAAAGACAGAGTGGTGAAGGGGGGTGAAGAGGTGTTTGTCAGTGACA
TAACCTATGTAAAATCAGACGAAGGAACTCACTATTTATCATTAGTCACAGATGCATATTCAAGAAAAATAATGGGTTATGAATTAAGTGATGAAATGAA
AGCCAGTGATGTCGTTAAAGCATTGGAGATGACGATAAAGAATCGTCAGACAACCACTGATGTCATTCATCATTCAGATAGAGGGATACAGTACTGCTCA
GCAGAATATCAACATAAATTGGCTGCGAATGCGATAAGGCCATCGATGACAGATGGGTATGATTGTTATCAGAATGCGTTAGCTGAGCGAGTGAATGGTA
TTTTGAAGCAAGAGTTTTTACTTTACCGCTGTCGTACGATGAAGGAGCTGGCAATACTCATCAAAGAATCGATTAGGACTTATAACGAGTTAAGACCGCA
CCTTAGTTTAGGAATGAAAACCCCAAACGAAGTGCATGAAAAAGCCAGTCGGGAGTTCCAACTGGCTTAATAAAAACCGTCAACCTATTTTAGGACTAGA
CA
TAAATTAGCGGTTGTTAGTCAAGTAGAAAAAGGCGAGCTAACGTATAAGCAAGCTCAAGACCATTATGGCATTCAAGGGAGAAGTACCGTCCTAACATGG
TTACGAAAACATGGTAGATTAGATTGGTCCCAGCCGATTGAGCATTCACCTATGTCCAAATCTACAGAAACACCCGCCCAGAAAATCAAACGATTAGAGA
AACAAGTCTCCAATCTCGAAATGAAAAATATGATTTATGGCGATATGGTCGAGTTACTTAAAAATGAGTACGGTATTGATTTAGAAAAAAAGTACTTAGC
CGAACGCTCTGGCTTGCCAAAGAAAAAGGCACTGTAAAGCTAGCGACAGCGAGTCGGCAGTTTAACCTATCAAGACAAGCTGTTTATCAATGGAAGCAGC
GCTTAGCAGCAAGAGCTGACATGTTAAAACCGGTGATGACGATGGTTATGTATTGGCGTCAGTTCATGCCCAGAGTGGGTACGCGTAAGCTTTATCAACT
CATCAAGCCACAGTTACTTAAACAAGGCATAAAGCTAGGTAGGGACGGCCTATTTCGGTATTTGAAACAACACAATATGTTAGTAAGGCCTAGGAAGAAT
TACACCAAGACAACCCATAGCCATCATTGGTTGAGAAAACACCCAAACTTACTCAAAGACAGAGTGGTGAAGGGGGGTGAAGAGGTGTTTGTCAGTGACA
TAACCTATGTAAAATCAGACGAAGGAACTCACTATTTATCATTAGTCACAGATGCATATTCAAGAAAAATAATGGGTTATGAATTAAGTGATGAAATGAA
AGCCAGTGATGTCGTTAAAGCATTGGAGATGACGATAAAGAATCGTCAGACAACCACTGATGTCATTCATCATTCAGATAGAGGGATACAGTACTGCTCA
GCAGAATATCAACATAAATTGGCTGCGAATGCGATAAGGCCATCGATGACAGATGGGTATGATTGTTATCAGAATGCGTTAGCTGAGCGAGTGAATGGTA
TTTTGAAGCAAGAGTTTTTACTTTACCGCTGTCGTACGATGAAGGAGCTGGCAATACTCATCAAAGAATCGATTAGGACTTATAACGAGTTAAGACCGCA
CCTTAGTTTAGGAATGAAAACCCCAAACGAAGTGCATGAAAAAGCCAGTCGGGAGTTCCAACTGGCTTAATAAAAACCGTCAACCTATTTTAGGACTAGA
CA
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 | |
|---|---|---|---|---|---|
| 396 bp | 131 aa | 42 | 437 | + | No |
Description : First part of the transposase
ORF sequence :
MKPSVSINIKRTQRDYTLGFKLAVVSQVEKGELTYKQAQDHYGIQGRSTVLTWLRKHGRLDWSQPIEHSPMSKSTETPAQKIKRLEKQVSNLEMKNMIYG
DMVELLKNEYGIDLEKKYLAERSGLPKKKAL
DMVELLKNEYGIDLEKKYLAERSGLPKKKAL
Blast result :ORF 2
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 891 bp | 296 aa | 380 | 1270 | + | No |
Description : Second part of the transposase
ORF sequence :
FRKKVLSRTLWLAKEKGTVKLATASRQFNLSRQAVYQWKQRLAARADMLKPVMTMVMYWRQFMPRVGTRKLYQLIKPQLLKQGIKLGRDGLFRYLKQHNM
LVRPRKNYTKTTHSHHWLRKHPNLLKDRVVKGGEEVFVSDITYVKSDEGTHYLSLVTDAYSRKIMGYELSDEMKASDVVKALEMTIKNRQTTTDVIHHSD
RGIQYCSAEYQHKLAANAIRPSMTDGYDCYQNALAERVNGILKQEFLLYRCRTMKELAILIKESIRTYNELRPHLSLGMKTPNEVHEKASREFQLA
LVRPRKNYTKTTHSHHWLRKHPNLLKDRVVKGGEEVFVSDITYVKSDEGTHYLSLVTDAYSRKIMGYELSDEMKASDVVKALEMTIKNRQTTTDVIHHSD
RGIQYCSAEYQHKLAANAIRPSMTDGYDCYQNALAERVNGILKQEFLLYRCRTMKELAILIKESIRTYNELRPHLSLGMKTPNEVHEKASREFQLA
Blast result :ORF 3
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1229 bp | 409 aa | 42 | 1270 | + | Yes |
Chemistry : DDE
ORF sequence :
MKPSVSINIKRTQRDYTLGFKLAVVSQVEKGELTYKQAQDHYGIQGRSTVLTWLRKHGRLDWSQPIEHSPMSKSTETPAQKIKRLEKQVSNLEMKNMIYG
DMVELLKNEYGIDLEKKVLSRTLWLAKEKGTVKLATASRQFNLSRQAVYQWKQRLAARADMLKPVMTMVMYWRQFMPRVGTRKLYQLIKPQLLKQGIKLG
RDGLFRYLKQHNMLVRPRKNYTKTTHSHHWLRKHPNLLKDRVVKGGEEVFVSDITYVKSDEGTHYLSLVTDAYSRKIMGYELSDEMKASDVVKALEMTIK
NRQTTTDVIHHSDRGIQYCSAEYQHKLAANAIRPSMTDGYDCYQNALAERVNGILKQEFLLYRCRTMKELAILIKESIRTYNELRPHLSLGMKTPNEVHE
KASREFQLA
DMVELLKNEYGIDLEKKVLSRTLWLAKEKGTVKLATASRQFNLSRQAVYQWKQRLAARADMLKPVMTMVMYWRQFMPRVGTRKLYQLIKPQLLKQGIKLG
RDGLFRYLKQHNMLVRPRKNYTKTTHSHHWLRKHPNLLKDRVVKGGEEVFVSDITYVKSDEGTHYLSLVTDAYSRKIMGYELSDEMKASDVVKALEMTIK
NRQTTTDVIHHSDRGIQYCSAEYQHKLAANAIRPSMTDGYDCYQNALAERVNGILKQEFLLYRCRTMKELAILIKESIRTYNELRPHLSLGMKTPNEVHE
KASREFQLA
Blast result :
Comments
There are 3 full length and 1 truncated copies of ISShfr4 encoded in the Shewanella frigidimarina chromosome. Orf1 and Orf2 are predicted to undergo programmed frameshifting to produce Orf3. The ISShfr4 transposase has 59% identity to ISShes2.
References
1] Romine, M. F. (2008) Direct submission.