ISBlo3
- Family IS3
- Group
Isoform Synonym(s)
| Accession number | Transposition | Origin | Host |
|---|---|---|---|
| NC_004307 | ND | Bifidobacterium longum | Bifidobacterium longum NCC2705 |
DNA section
IS Length : 1480 bp
Ends
IR Length : 22/24
IRL : TGAACCGCACCCCGATTGTTGGACTGAAGTAATTCAGATTCGATGATCGG
IRR : TGAACTGCGCCCCGATTGTTGGACGTGGTTTATTAAGGGTACCTGATTAG
Insertion site
| Left flank | Direct repeat | Right flank | DR Length |
|---|---|---|---|
| CCCCGAGTGA | GAATTGG | ACTCACGACC | 7 |
DNA sequence
TGAACCGCACCCCGATTGTTGGACTGAAGTAATTCAGATTCGATGATCGGAGGTGCGGTTTCTCATGTGTAGGGATCGCAGGCGTCATTACGATGACGGT
TTCATGCGGGTCGTCGCCGACCTGATCCGGGGCGGGGCCGGGAGGCGTTCTCTCGCCCGCCGGCTTGGCGTGCCCGTCAGTACCGCGGGAAAATGGGTGT
TGTCATACCGGTTTGGCGGGGAGGCGGCGCTCATGGGAGAACGCGAAGGCAACAGGAGATACGACTACGAGACGAAGCTCGCGGCGGTGCGCGACCATGT
GGAGCATGGGCTGACGAAGGCCGAAGTCATGGAGAAGTACAGGATCGCGGGTCCCGCCCCGTTGGAGCGCTGGTGCCGCGAGTACCGGTCCGGCGGCCCG
GACGCGCTGCGTCCGAAACCGAAGGGCAGGCCCAGGGGCGCGAAATCCAAGCCGAGGCCGGCTCCCACAAGGGAACAGCTCCTTGAGGAGGAGAACGCGT
ACCTCAAGGCGAGGGTCGCGTACCTGGAAAAAGTCGACGCCCTGCTGGCGTGGAGATCGGCAACCGGGACAGAACGGTGATCGTCTCCATGCTGGCGGGG
CTGGGACATCGGCTCCGGCACCTGCTCAGGGCGGCCGGACTGGCGAAAAGCACGTATTACCATCTTCTGTCGCATCCGGCCGCCGTGACCCGGCCGGACC
TCGAGCCGATGGTCGCCGAGATATTCGCGCGCACGCCCAACGGGTGCGGCCACCGGCAGATACGCATGTGCCTCGTGCACGAGTTCGGGGTGCGGGTGAG
CCACAAGAGCGTGCTGAAGGTCATGAGGCGCATGGGCCTGGAATGCCGGATACGCAGGCCGAACCCGTACCGGAAATACAGCTCGTACCGGGACGAGACG
GGCGCGAGGGCGGAGAACCTGCTGAACCGCGACTTCACGGCCGACCGGCCGTGGGTGAAGCTGGGCACGGACGTCACCGAGTTCAGGGTCGCCGACGGCA
AGGCGTATCCGGCTCCCGTATGCGACATGGGATCCAAGGAGATCGTGGCCTGGGACGTCAGCCGGCATCCCGACATGGCCCAGCAGCGGCGCCTGCTCGC
CATGCTCGAGGAGAAGCTGCCCGAAGACGCCGACCCGATCCCGCACTCCGACATGGGCTGGCAGTACCGGCACCGGTGGTGGCGCGACCGGCTCGCGGGA
CTGAACATCCGCCAGTCCATGAGCAGGAAGGGCAACTGCATCGACAACGCCGCGACCGAGCAGGTGTTCGGCCACCTCAAGGACGAGTTCCACGCCGGAC
GCGAGTTCGCCTCATACGAACAGTTCAAGAACGAACTGGACGCGTACATCATCCACTGGAACACCAAACGCCGCCAGATACGACTGGAGGGACACACCCC
GGAGGAATTCCGGAACATGTCCCCCACAGCCTAATCAGGTACCCTTAATAAACCACGTCCAACAATCGGGGCGCAGTTCA
TTCATGCGGGTCGTCGCCGACCTGATCCGGGGCGGGGCCGGGAGGCGTTCTCTCGCCCGCCGGCTTGGCGTGCCCGTCAGTACCGCGGGAAAATGGGTGT
TGTCATACCGGTTTGGCGGGGAGGCGGCGCTCATGGGAGAACGCGAAGGCAACAGGAGATACGACTACGAGACGAAGCTCGCGGCGGTGCGCGACCATGT
GGAGCATGGGCTGACGAAGGCCGAAGTCATGGAGAAGTACAGGATCGCGGGTCCCGCCCCGTTGGAGCGCTGGTGCCGCGAGTACCGGTCCGGCGGCCCG
GACGCGCTGCGTCCGAAACCGAAGGGCAGGCCCAGGGGCGCGAAATCCAAGCCGAGGCCGGCTCCCACAAGGGAACAGCTCCTTGAGGAGGAGAACGCGT
ACCTCAAGGCGAGGGTCGCGTACCTGGAAAAAGTCGACGCCCTGCTGGCGTGGAGATCGGCAACCGGGACAGAACGGTGATCGTCTCCATGCTGGCGGGG
CTGGGACATCGGCTCCGGCACCTGCTCAGGGCGGCCGGACTGGCGAAAAGCACGTATTACCATCTTCTGTCGCATCCGGCCGCCGTGACCCGGCCGGACC
TCGAGCCGATGGTCGCCGAGATATTCGCGCGCACGCCCAACGGGTGCGGCCACCGGCAGATACGCATGTGCCTCGTGCACGAGTTCGGGGTGCGGGTGAG
CCACAAGAGCGTGCTGAAGGTCATGAGGCGCATGGGCCTGGAATGCCGGATACGCAGGCCGAACCCGTACCGGAAATACAGCTCGTACCGGGACGAGACG
GGCGCGAGGGCGGAGAACCTGCTGAACCGCGACTTCACGGCCGACCGGCCGTGGGTGAAGCTGGGCACGGACGTCACCGAGTTCAGGGTCGCCGACGGCA
AGGCGTATCCGGCTCCCGTATGCGACATGGGATCCAAGGAGATCGTGGCCTGGGACGTCAGCCGGCATCCCGACATGGCCCAGCAGCGGCGCCTGCTCGC
CATGCTCGAGGAGAAGCTGCCCGAAGACGCCGACCCGATCCCGCACTCCGACATGGGCTGGCAGTACCGGCACCGGTGGTGGCGCGACCGGCTCGCGGGA
CTGAACATCCGCCAGTCCATGAGCAGGAAGGGCAACTGCATCGACAACGCCGCGACCGAGCAGGTGTTCGGCCACCTCAAGGACGAGTTCCACGCCGGAC
GCGAGTTCGCCTCATACGAACAGTTCAAGAACGAACTGGACGCGTACATCATCCACTGGAACACCAAACGCCGCCAGATACGACTGGAGGGACACACCCC
GGAGGAATTCCGGAACATGTCCCCCACAGCCTAATCAGGTACCCTTAATAAACCACGTCCAACAATCGGGGCGCAGTTCA
Recoding section
- Recoding by frameshift
- Frame -1
- Type translational
- Experimentally demonstrated No
Stimulators :
- Shine-Dalgarno sequence :
- Secondary structure :
Recoding motif :
AAAAAG
Protein section
ORF number : 3
ORF 1
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 516 bp | 171 aa | 65 | 580 | + | No |
Description : First part of the transposase
ORF sequence :
MCRDRRRHYDDGFMRVVADLIRGGAGRRSLARRLGVPVSTAGKWVLSYRFGGEAALMGEREGNRRYDYETKLAAVRDHVEHGLTKAEVMEKYRIAGPAPL
ERWCREYRSGGPDALRPKPKGRPRGAKSKPRPAPTREQLLEEENAYLKARVAYLEKVDALLAWRSATGTER
ERWCREYRSGGPDALRPKPKGRPRGAKSKPRPAPTREQLLEEENAYLKARVAYLEKVDALLAWRSATGTER
Blast result :ORF 2
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 855 bp | 284 aa | 580 | 1434 | + | No |
Description : Second part of the transposase
ORF sequence :
IVSMLAGLGHRLRHLLRAAGLAKSTYYHLLSHPAAVTRPDLEPMVAEIFARTPNGCGHRQIRMCLVHEFGVRVSHKSVLKVMRRMGLECRIRRPNPYRKY
SSYRDETGARAENLLNRDFTADRPWVKLGTDVTEFRVADGKAYPAPVCDMGSKEIVAWDVSRHPDMAQQRRLLAMLEEKLPEDADPIPHSDMGWQYRHRW
WRDRLAGLNIRQSMSRKGNCIDNAATEQVFGHLKDEFHAGREFASYEQFKNELDAYIIHWNTKRRQIRLEGHTPEEFRNMSPTA
SSYRDETGARAENLLNRDFTADRPWVKLGTDVTEFRVADGKAYPAPVCDMGSKEIVAWDVSRHPDMAQQRRLLAMLEEKLPEDADPIPHSDMGWQYRHRW
WRDRLAGLNIRQSMSRKGNCIDNAATEQVFGHLKDEFHAGREFASYEQFKNELDAYIIHWNTKRRQIRLEGHTPEEFRNMSPTA
Blast result :ORF 3
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1370 bp | 457 aa | 65 | 1434 | + | Yes |
Chemistry : DDE
ORF sequence :
MCRDRRRHYDDGFMRVVADLIRGGAGRRSLARRLGVPVSTAGKWVLSYRFGGEAALMGEREGNRRYDYETKLAAVRDHVEHGLTKAEVMEKYRIAGPAPL
ERWCREYRSGGPDALRPKPKGRPRGAKSKPRPAPTREQLLEEENAYLKARVAYLEKKSRRPAGVEIGNRDRTVIVSMLAGLGHRLRHLLRAAGLAKSTYY
HLLSHPAAVTRPDLEPMVAEIFARTPNGCGHRQIRMCLVHEFGVRVSHKSVLKVMRRMGLECRIRRPNPYRKYSSYRDETGARAENLLNRDFTADRPWVK
LGTDVTEFRVADGKAYPAPVCDMGSKEIVAWDVSRHPDMAQQRRLLAMLEEKLPEDADPIPHSDMGWQYRHRWWRDRLAGLNIRQSMSRKGNCIDNAATE
QVFGHLKDEFHAGREFASYEQFKNELDAYIIHWNTKRRQIRLEGHTPEEFRNMSPTA
ERWCREYRSGGPDALRPKPKGRPRGAKSKPRPAPTREQLLEEENAYLKARVAYLEKKSRRPAGVEIGNRDRTVIVSMLAGLGHRLRHLLRAAGLAKSTYY
HLLSHPAAVTRPDLEPMVAEIFARTPNGCGHRQIRMCLVHEFGVRVSHKSVLKVMRRMGLECRIRRPNPYRKYSSYRDETGARAENLLNRDFTADRPWVK
LGTDVTEFRVADGKAYPAPVCDMGSKEIVAWDVSRHPDMAQQRRLLAMLEEKLPEDADPIPHSDMGWQYRHRWWRDRLAGLNIRQSMSRKGNCIDNAATE
QVFGHLKDEFHAGREFASYEQFKNELDAYIIHWNTKRRQIRLEGHTPEEFRNMSPTA
Blast result :
Comments
A potential sequence for translational frameshift is present around position 530 (GGAAAAAGTC).
Two complete copies of the element are found in the genome of NCC2705. Three remnants of the left end including the IR (119 bp, 86 bp, and 60 bp) suggest that three others copies have been truncated.
Coordinates:
ISBlo3a complement(585186..586665)
ISBlo3b complement(1792294..1793773)
ISBlo3c 356354..356472
ISBlo3d complement(785664..785749)
ISBlo3e complement(1850052..1850111)
DR :
One copy shows a 7 bp target duplication
Identity between IS copies:
ISBlo3a 100%
ISBlo3b 99.3%
ISBlo3c 92.5% (119 bp)
ISBlo3d 94.3% (86 bp)
ISBlo3e 98.4% (60 bp)
Two complete copies of the element are found in the genome of NCC2705. Three remnants of the left end including the IR (119 bp, 86 bp, and 60 bp) suggest that three others copies have been truncated.
Coordinates:
ISBlo3a complement(585186..586665)
ISBlo3b complement(1792294..1793773)
ISBlo3c 356354..356472
ISBlo3d complement(785664..785749)
ISBlo3e complement(1850052..1850111)
DR :
One copy shows a 7 bp target duplication
Identity between IS copies:
ISBlo3a 100%
ISBlo3b 99.3%
ISBlo3c 92.5% (119 bp)
ISBlo3d 94.3% (86 bp)
ISBlo3e 98.4% (60 bp)
References
1] Schell,M.A., Karmirantzou,M., Snel,B., Vilanova,D., Berger,B., Pessi,G., Zwahlen,M.-C., Desiere,F., Bork,P., Delley,M., Pridmore,D. and Arigoni,F. (2002)Proc. Natl. Acad. Sci. U.S.A. 99 (22), 14422-14427