ISCod1
- Family IS3
- Group IS150
Isoform Synonym(s)
| Accession number | Transposition | Origin | Host |
|---|---|---|---|
| NC_002935 | ND | Corynebacterium diphtheriae | Corynebacterium diphtheriae NCTC 13129 |
DNA section
IS Length : 1438 bp
Ends
IR Length : 21/26
IRL : TGAACTGCTCCCCATTAGTTGGACTGAGAAATCAGTTTCCGACTATTGGG
IRR : TGAACTAGCCCCCGAAAGTTGGACTGGTTTAATTCTATGCGGTTAGTGGT
Insertion site
| Left flank | Direct repeat | Right flank | DR Length |
|---|---|---|---|
| CGTGGGGCAG | GTTTTTCGTC | 0 |
DNA sequence
TGAACTGCTCCCCATTAGTTGGACTGAGAAATCAGTTTCCGACTATTGGGGAGTATTTCTTTGAGAGCACGAAGTTCTCTAAGTCAGTGGCAGCGGGAGC
AGCTCGTTGACTTGTTTGAGCAGGGACTGGGCTACGGCGCAGCGGCTCGTCGAATGGGCGTTAGCAAGTACGCGGTGCGAATGCTTCAACGTCGATTCAA
ACTTCATGGCAGGGCTGTGTCTTGTGGAGAATCCAACGAAGCAGCACTATTCCTTCGAAGTTAGAAAACAGGTCGTCGATCGTTTCAACGCTGGCCAATC
CAAGATGGACCTTGCCCGGGAATTCGGGTTATCTTCGGACCAGCTTGTCTCCAGTTGGGTGCGTGCCTGGCGTGCAGGTGGTGATGAGGCACTTCGGCCG
AAACCGAAGGGCAGGCCTAAAGGTAGCGCCAGTTCGAAGCCATTGACTGAGGAAGACCGGCTGCGCCGTGAGGTGGAGAAACTACGCGCAGAAAACGCGT
ACTTAAAAAAATTGCGGGACTTGAGGAACCAGCGACGAAGCTAAGAGTCGAAGCGATCGTCATCCTCAAGTCTGACCATCGACTAGAAGACTTATTGGAC
GCGGCAGGTCTTGCCCGATCAACATTTTTCTATCACCAGCAACGCCTAAACGTGCCGGATAAGCATATCGACCTCAAGGAAGCGATCGTCGAGGTCTTCA
CGCGGACGAACCGTCGTTACGGCTACCGCAGGATTCATGCTCACCTTCGCCAAGACGGATGGAATGTCAACCATAAGCTGGTCTACAAGCTCATGGACGA
GCTAGGCCTTAAATCCAAGGTCAGAGCAAAGAAGAGGTACAACGCCTACCAAGGTACTGTCAGTCACATCGCGGAGAATGTGCTGGATCGATGCTTCACG
CCCGATAAACCAAACACGGTGTGGACGAGTGATGTCACCGAGTTTCGCATTGCCGGCACCAAGGTCTACCTGTCACCAATCATGGATCTCTATGACCGCT
CAATTGTGTCATATAGTGTGTCTACCTCACCAAATACAGCATTTACGTCAAGGTCATTGAAAGATGCCATCACAAGCCAATCTCCCGGAAGCGGCTTACT
GGTACACACAGATCAAGGGATCCAGTACCAACATTCCAGCTGGCGTGACCTCATCACAAGTATTGACGGCATCCAATCGATGTCCAGGAAAGGCAACTGC
TACGACAATGCTGTAATGGAAAACTTCTTCGGACACCTCAAGTCAGAGATGCACCACGGTGAATCATTCGACGGTCTCGAGCACTTCAGACAGGCCCTGG
ATGGGTACATCCACTGGTATAACCACGAACGCATTCAGAAACGGCTCAAGGGCCTGGCCCCGATGCAATACCGGAACCAGACCCTTGAACCACTAACCGC
ATAGAATTAAACCAGTCCAACTTTCGGGGGCTAGTTCA
AGCTCGTTGACTTGTTTGAGCAGGGACTGGGCTACGGCGCAGCGGCTCGTCGAATGGGCGTTAGCAAGTACGCGGTGCGAATGCTTCAACGTCGATTCAA
ACTTCATGGCAGGGCTGTGTCTTGTGGAGAATCCAACGAAGCAGCACTATTCCTTCGAAGTTAGAAAACAGGTCGTCGATCGTTTCAACGCTGGCCAATC
CAAGATGGACCTTGCCCGGGAATTCGGGTTATCTTCGGACCAGCTTGTCTCCAGTTGGGTGCGTGCCTGGCGTGCAGGTGGTGATGAGGCACTTCGGCCG
AAACCGAAGGGCAGGCCTAAAGGTAGCGCCAGTTCGAAGCCATTGACTGAGGAAGACCGGCTGCGCCGTGAGGTGGAGAAACTACGCGCAGAAAACGCGT
ACTTAAAAAAATTGCGGGACTTGAGGAACCAGCGACGAAGCTAAGAGTCGAAGCGATCGTCATCCTCAAGTCTGACCATCGACTAGAAGACTTATTGGAC
GCGGCAGGTCTTGCCCGATCAACATTTTTCTATCACCAGCAACGCCTAAACGTGCCGGATAAGCATATCGACCTCAAGGAAGCGATCGTCGAGGTCTTCA
CGCGGACGAACCGTCGTTACGGCTACCGCAGGATTCATGCTCACCTTCGCCAAGACGGATGGAATGTCAACCATAAGCTGGTCTACAAGCTCATGGACGA
GCTAGGCCTTAAATCCAAGGTCAGAGCAAAGAAGAGGTACAACGCCTACCAAGGTACTGTCAGTCACATCGCGGAGAATGTGCTGGATCGATGCTTCACG
CCCGATAAACCAAACACGGTGTGGACGAGTGATGTCACCGAGTTTCGCATTGCCGGCACCAAGGTCTACCTGTCACCAATCATGGATCTCTATGACCGCT
CAATTGTGTCATATAGTGTGTCTACCTCACCAAATACAGCATTTACGTCAAGGTCATTGAAAGATGCCATCACAAGCCAATCTCCCGGAAGCGGCTTACT
GGTACACACAGATCAAGGGATCCAGTACCAACATTCCAGCTGGCGTGACCTCATCACAAGTATTGACGGCATCCAATCGATGTCCAGGAAAGGCAACTGC
TACGACAATGCTGTAATGGAAAACTTCTTCGGACACCTCAAGTCAGAGATGCACCACGGTGAATCATTCGACGGTCTCGAGCACTTCAGACAGGCCCTGG
ATGGGTACATCCACTGGTATAACCACGAACGCATTCAGAAACGGCTCAAGGGCCTGGCCCCGATGCAATACCGGAACCAGACCCTTGAACCACTAACCGC
ATAGAATTAAACCAGTCCAACTTTCGGGGGCTAGTTCA
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 | |
|---|---|---|---|---|---|
| 438 bp | 145 aa | 110 | 547 | + | No |
Description : First part of the transposase
ORF sequence :
MTCLSRDWATAQRLVEWALASTRCECFNVDSNFMAGLCLVENPTKQHYSFEVRKQVVDRFNAGQSKMDLAREFGLSSDQLVSSWVRAWRAGGDEALRPKP
KGRPKGSASSKPLTEEDRLRREVEKLRAENAYLKKLRDLRNQRRS
KGRPKGSASSKPLTEEDRLRREVEKLRAENAYLKKLRDLRNQRRS
Blast result :ORF 2
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 933 bp | 310 aa | 472 | 1404 | + | No |
Description : Second part of the transposase
ORF sequence :
GGETTRRKRVLKKIAGLEEPATKLRVEAIVILKSDHRLEDLLDAAGLARSTFFYHQQRLNVPDKHIDLKEAIVEVFTRTNRRYGYRRIHAHLRQDGWNVN
HKLVYKLMDELGLKSKVRAKKRYNAYQGTVSHIAENVLDRCFTPDKPNTVWTSDVTEFRIAGTKVYLSPIMDLYDRSIVSYSVSTSPNTAFTSRSLKDAI
TSQSPGSGLLVHTDQGIQYQHSSWRDLITSIDGIQSMSRKGNCYDNAVMENFFGHLKSEMHHGESFDGLEHFRQALDGYIHWYNHERIQKRLKGLAPMQY
RNQTLEPLTA
HKLVYKLMDELGLKSKVRAKKRYNAYQGTVSHIAENVLDRCFTPDKPNTVWTSDVTEFRIAGTKVYLSPIMDLYDRSIVSYSVSTSPNTAFTSRSLKDAI
TSQSPGSGLLVHTDQGIQYQHSSWRDLITSIDGIQSMSRKGNCYDNAVMENFFGHLKSEMHHGESFDGLEHFRQALDGYIHWYNHERIQKRLKGLAPMQY
RNQTLEPLTA
Blast result :ORF 3
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1295 bp | 432 aa | 110 | 1404 | + | Yes |
Chemistry : DDE
ORF sequence :
MTCLSRDWATAQRLVEWALASTRCECFNVDSNFMAGLCLVENPTKQHYSFEVRKQVVDRFNAGQSKMDLAREFGLSSDQLVSSWVRAWRAGGDEALRPKP
KGRPKGSASSKPLTEEDRLRREVEKLRAENAYLKKIAGLEEPATKLRVEAIVILKSDHRLEDLLDAAGLARSTFFYHQQRLNVPDKHIDLKEAIVEVFTR
TNRRYGYRRIHAHLRQDGWNVNHKLVYKLMDELGLKSKVRAKKRYNAYQGTVSHIAENVLDRCFTPDKPNTVWTSDVTEFRIAGTKVYLSPIMDLYDRSI
VSYSVSTSPNTAFTSRSLKDAITSQSPGSGLLVHTDQGIQYQHSSWRDLITSIDGIQSMSRKGNCYDNAVMENFFGHLKSEMHHGESFDGLEHFRQALDG
YIHWYNHERIQKRLKGLAPMQYRNQTLEPLTA
KGRPKGSASSKPLTEEDRLRREVEKLRAENAYLKKIAGLEEPATKLRVEAIVILKSDHRLEDLLDAAGLARSTFFYHQQRLNVPDKHIDLKEAIVEVFTR
TNRRYGYRRIHAHLRQDGWNVNHKLVYKLMDELGLKSKVRAKKRYNAYQGTVSHIAENVLDRCFTPDKPNTVWTSDVTEFRIAGTKVYLSPIMDLYDRSI
VSYSVSTSPNTAFTSRSLKDAITSQSPGSGLLVHTDQGIQYQHSSWRDLITSIDGIQSMSRKGNCYDNAVMENFFGHLKSEMHHGESFDGLEHFRQALDG
YIHWYNHERIQKRLKGLAPMQYRNQTLEPLTA
Blast result :
Comments
ISCod1 is 63 % (ORFA) aa similar to IS861 and 66% (ORFB) aa similar to ISEnfa3. The third ORF is a putative ORFAB transposase reconstructed in sillico by -1 frameshift.
References
1] Cerdeno-Tarraga,A.M., Efstratiou,A., Dover,L.G., Holden,M.T.G., Pallen,M., Bentley,S.D., Besra,G.S., Churcher,C., James,K.D., De Zoysa,A., Chillingworth,T., Cronin,A., Dowd,L., Feltwell,T., Hamlin,N., Holroyd,S., Jagels,K., Moule,S., Quail,M.A., Rabbinowitsch,E., Rutherford,K., Thomson,N.R., Unwin,L., Whitehead,S. and Barrell B.G. Parkhill,J. (2003) Nucleic Acids Res. 31 (22), 6516-6523.