ISfinder Mirror Site

IS1096

Family ISL3
Group

MGE type ISRelated element(s) :
Isoform Synonym(s)

Accession number	Transposition	Origin	Host
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 flank	Direct repeat	Right flank	DR Length
NNNNNNNNNC	GGTTTTCT	NNNNNNNNNN	8
NNNNNNNNNN	CGATAACG	NNNNNNNNNN	8
NNNNNNNNNN	GTTTTGCG	NNNNNNNNNN	8
NNNNNNNNNN	TCATTCGA	NNNNNNNNNN	8
NNNNNNNNNN	GTGTTCCC	NNNNNNNNNN	8
NNNNNNNNNN	CGATAAGG	NNNNNNNNNN	8
NNNNNNNNNN	GGTTTCCC	NNNNNNNNNN	8
NNNNNNNNNN	GCTAAACC	NNNNNNNNNN	8
NNNNNNNNNN	CTCAATGA	NNNNNNNNNN	8
NNNNNNNNNN	CCATAACT	NNNNNNNNNN	8

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

Length		Begin	End	Strand	Fusion ORF
1242 bp	412 aa	193	1434	+	No

ORF function : Transposase
Chemistry : Unknow

ORF sequence :

MTGQRLDPDRAVLACRVADEDRWCRRCGEEGVVRDSVTRTLAHEPFGWRPTALLVTIRRYRCAGCAHVWRQDASAAAEPRARLSRRALRWALEALVCQHL
SVARVAEALAVSWNTANNAVLAEGQRVLIADPARFDGVAVIGVDEHVWRHTRRGDKYVTVIIDLTPVRDGTGPARLLDMVEGRSKKAFADWLAQRPQEWR
DRVDVVAMDGFSGFKTAATEELPDAATVMDPFHVVRLAGNALDECRRRVQLATCGHRGRSTDPLYRSRRTLHTGADLLTDRQKARLAALFAANAHAEIEA
TWAMYQRTVAAYREPDRTKGRTMMAALITTLSTGVPTSLTELITLGRTLKKRAADVLAYFDRPGTSNGPTEAINGRLEHLRGSALGFRNLTNYIARSLLE
TGGFRTQLRQPR

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
714 bp	237 aa	1470	2183	-	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.