IS1096

  • Family ISL3
  • Group
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
M76495 Y Mycobacterium smegmatis
Mycobacterium smegmatis ATCC27204
Mycobacterium smegmatis ATCC607
Mycobacterium smegmatis ATCC27199
DNA section
IS Length : 2259 bp

Ends


IR Length : 24/26

IRL : GGCTCTTCGCAGTTGAGGGTGTAGAGGTCGTCGGCGCGTCGGTGCCGGGA
IRR : GGCTCTTCGCACTTGACGGTGTAGAGACGATCAGCTGCTTTCGCGCTGTG

Insertion site


Left flankDirect repeatRight flankDR Length
NNNNNNNNNCGGTTTTCTNNNNNNNNNN8
NNNNNNNNNNCGATAACGNNNNNNNNNN8
NNNNNNNNNNGTTTTGCGNNNNNNNNNN8
NNNNNNNNNNTCATTCGANNNNNNNNNN8
NNNNNNNNNNGTGTTCCCNNNNNNNNNN8
NNNNNNNNNNCGATAAGGNNNNNNNNNN8
NNNNNNNNNNGGTTTCCCNNNNNNNNNN8
NNNNNNNNNNGCTAAACCNNNNNNNNNN8
NNNNNNNNNNCTCAATGANNNNNNNNNN8
NNNNNNNNNNCCATAACTNNNNNNNNNN8

DNA sequence

GGCTCTTCGCAGTTGAGGGTGTAGAGGTCGTCGGCGCGTCGGTGCCGGGATAGGGGTCGAGGTCTTCCGATGATGGAGGTTCCTACGCCATCCATCTGAA
AGACCTCGACGTGCCTGACGCTACCGGTCGGTGCGGGCTTCGCCTGCGCTGACCTGACGACTTTCTGCCGCCTCGACGAGCTCGGGTTGGAGGTGACCGG
CCAACGCCTCGACCCTGATCGGGCCGTGCTGGCGTGCCGGGTCGCCGATGAGGATCGGTGGTGCCGCCGCTGCGGCGAAGAAGGCGTTGTACGTGACAGC
GTGACTCGCACGTTGGCTCATGAACCGTTCGGGTGGCGACCCACGGCTTTGCTGGTCACGATCCGCCGTTACCGTTGCGCCGGCTGCGCTCATGTGTGGC
GCCAGGATGCCAGCGCCGCAGCCGAACCGCGGGCCAGGCTGTCCCGGCGTGCTCTGCGGTGGGCGCTGGAAGCCCTTGTCTGCCAACACCTGTCGGTGGC
CCGGGTCGCCGAGGCGCTTGCGGTGTCGTGGAACACTGCCAACAACGCCGTGCTCGCCGAAGGTCAGCGGGTGCTCATCGCCGATCCGGCCCGGTTCGAT
GGCGTCGCGGTGATCGGCGTCGATGAGCACGTGTGGCGGCACACTCGCCGCGGCGACAAGTACGTCACCGTCATCATCGATCTCACGCCCGTGCGTGACG
GGACCGGCCCCGCACGGCTGCTCGACATGGTGGAGGGCCGCTCCAAGAAGGCGTTCGCCGACTGGCTGGCACAGCGGCCACAGGAGTGGCGTGATCGTGT
GGACGTTGTTGCCATGGACGGGTTCTCCGGGTTCAAGACCGCCGCCACCGAAGAACTGCCTGACGCGGCCACGGTGATGGACCCCTTCCACGTGGTCCGC
CTGGCCGGCAACGCCCTCGACGAGTGCCGACGCCGCGTGCAGCTGGCCACCTGCGGGCACCGCGGCCGCAGCACCGACCCGCTCTACCGATCGCGACGCA
CCCTGCACACCGGGGCCGACCTGCTCACCGACCGCCAGAAAGCCCGACTGGCCGCACTGTTCGCCGCCAACGCGCACGCCGAGATCGAGGCCACCTGGGC
GATGTATCAACGCACCGTGGCCGCCTACCGCGAACCAGACCGCACCAAGGGCCGCACCATGATGGCTGCACTGATCACCACGCTGAGCACAGGCGTCCCC
ACGTCGCTGACCGAGCTGATCACCCTCGGGCGGACACTGAAGAAGCGTGCCGCCGACGTCCTGGCCTACTTCGACCGCCCCGGCACCTCCAACGGGCCGA
CCGAAGCGATCAACGGCCGCCTCGAACACCTGCGCGGATCCGCCCTGGGCTTCCGCAACCTCACCAACTACATCGCCCGGTCCCTGCTCGAGACCGGAGG
CTTCCGAACCCAGCTCCGTCAACCTCGGCGGTGAAGAATCCTCAACGCGTGTTCAACGCGGCCAGAGCGTCATTGGTCTCGGCCACCGAGAAACGGTCGG
GGTGCCAGCCCCGGGGGCAGCCAGTCCCTCATCTCCTGCGCACCGAGTCCCATCGGCGTTTCCCGCGGGTCGTACCCGCCGCGAACCCACGCAGCCAACT
CCTCATAGCCGCCCAGGCCACCACAGTCCTCCGGCGGACAGGCCATCTTTCCCGTCAGACACACCGCAGCCGGGGGCGGATCATCGAAAACGTCTTCGAC
CACGAGCACGTGGTCCCATCCGTCGCCGAAGTCGTAATCGTAGAACAACCGCTCGCCCTTATCGGACACCACCTGATCGAGGCGCACGCTGTCCTCGACG
ACACCGTCGTCGCCTTCGCTGAGATCAAACCCGGTGACGAAGTAGGCACGGGTCCGCCGGTCCGCCCCGACACCGAACTTATGCAGATGACTGTCCTGCC
AGCCCATAACGACCTGCAGCACAACATGGAGCTCATCGAGCATGAGGTCGCCCGGCAGGTCCAGCCGACGCCAGATCGGCGGCTTGGCGTACATCAGGTC
GACGCGCACCCGGAAGCCCCGCGCACGATCCGGCACCGCCCGCACCTCGGGCGTCGGCTCATCGAACATTCCCGCGAACACGTTCCGACCAGCGTCGGCC
ATTAGCTTCTGCAGCAACGCCAGGTCCACACTGCCCCCGGACACTCCGCTCTTCCTCTTGCTCTTCCGCTTCTTCTCCGGCACACCCCAAGCCAACCAGA
CCCCTCGATCACAGCGCGAAAGCAGCTGATCGTCTCTACACCGTCAAGTGCGAAGAGCC
Protein section
ORF number : 2

 

ORF 1
LengthBeginEndStrandFusion ORF
1242 bp412 aa1931434+No
ORF function : Transposase
Chemistry : Unknow

ORF sequence :

VTGQRLDPDRAVLACRVADEDRWCRRCGEEGVVRDSVTRTLAHEPFGWRPTALLVTIRRYRCAGCAHVWRQDASAAAEPRARLSRRALRWALEALVCQHL
SVARVAEALAVSWNTANNAVLAEGQRVLIADPARFDGVAVIGVDEHVWRHTRRGDKYVTVIIDLTPVRDGTGPARLLDMVEGRSKKAFADWLAQRPQEWR
DRVDVVAMDGFSGFKTAATEELPDAATVMDPFHVVRLAGNALDECRRRVQLATCGHRGRSTDPLYRSRRTLHTGADLLTDRQKARLAALFAANAHAEIEA
TWAMYQRTVAAYREPDRTKGRTMMAALITTLSTGVPTSLTELITLGRTLKKRAADVLAYFDRPGTSNGPTEAINGRLEHLRGSALGFRNLTNYIARSLLE
TGGFRTQLRQPR

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
714 bp237 aa14702183-No
ORF function : Passenger Gene
Annotation : TnpRDescription :

ORF sequence :

MPEKKRKSKRKSGVSGGSVDLALLQKLMADAGRNVFAGMFDEPTPEVRAVPDRARGFRVRVDLMYAKPPIWRRLDLPGDLMLDELHVVLQVVMGWQDSHL
HKFGVGADRRTRAYFVTGFDLSEGDDGVVEDSVRLDQVVSDKGERLFYDYDFGDGWDHVLVVEDVFDDPPPAAVCLTGKMACPPEDCGGLGGYEELAAWV
RGGYDPRETPMGLGAQEMRDWLPPGLAPRPFLGGRDQ

 

Blast result :
Comments
IS1096 transposition frequency is about 10-5. Several suicide vectors (Tn5367, Tn5368 and Tn5369) have been developed from IS1096, and these elements were shown to be active in Mycobacterium tuberculosis, albeit with a rather low transposition efficiency (McAdam et al., 1995). IS1096 harbours two large ORFs named TnpA, 412-aa (193-1434) and TnpR, 237-aa (1470-2183) CS. Whereas the TnpA is the transposase, TnpR shows similarities with two ORFs: 1] ORF3 (237-aa, 30 % identity) from Agrobacterium rhizogenes plasmid pRiA4 (Endoh et al., 1990, FEBS Lett. 271, 28-32. Accession. number X51418). This gene is located about 400 bp downstream the virA gene; 2] ORF91 (91-aa, partial, 30 % identity) from Rhizobium sp. symbiotic plasmid (Accession. number X74068). This gene is located about 700 bp from a nodulation gene.
References
1] Cirillo, J.D., Barletta, R.G., Bloom, B.R., and Jacobs, W.R., Jr. (1991) J. Bacteriol. 173, 7772-7780.
2] McAdam, R.A., Weisbrod, T.R., Martin, J., Scuderi, J.D., Brown, A.M., Cirillo, J.D., Bloom, B.R., and Jacobs, W.R., Jr. (1995) Inf. Immun. 63, 1004-1012.