ISRgn1
- Family IS3
- Group IS3
Isoform Synonym(s) ISRg1
| Accession number | Transposition | Origin | Host |
|---|---|---|---|
| AF320327 | ND | Ruminococcus gnavus | Ruminococcus gnavus |
DNA section
IS Length : 1278 bp
Ends
IR Length : 28/38
IRL : TGTTGTGATATAACATAGTTGTAACATCTCGACCTAATAAGATATAATCT
IRR : TGTTGTGGTCAAGCTTTTTTGTAACACTACGACCTAATTTCCACTACAGG
Insertion site
| Left flank | Direct repeat | Right flank | DR Length |
|---|---|---|---|
| CTTGCATAGA | TAC | CATATGTAAA | 3 |
DNA sequence
TGTTGTGATATAACATAGTTGTAACATCTCGACCTAATAAGATATAATCTTAGGAGGAAACGAGGTATGTTAAAGATGAGTCAATACTATGACCCAGAAT
TCAAGAAGAAGATAGTCCGTCTTCATCTTGAAGAGGGAAGATCCCTCAAAGGTCTTGCTGAAGAATATGGTGTATCCAAAGCAAGTATATCTATTTGGAC
AAAACAATTCCGTGAAGAATGCCAAACAAACGACGAAGCCAAAGCCGATTATGATTACATGAAAGAGAATCTACAGCTTAAAAAGCAACTTGCAGAACTC
CAAAAGGAAAATGACTTCTTAAAAAAAGCAGCGGCATTCTTTGCGAAGGAAATCGATTAGAGGCTTATCGATTCATTCAGAAATACAACAAAGACTTTGG
ACTCAGATGGCTTCTTAGAAAGTTTAACATCTGTCCAAATGCTTATTACAATTATCTAAAAAATCGAAAAGCTGATTATCATCAACAGAAAGATGAGATC
AAAGATTCCATTCGAGAAATCTATCATTCTCATGGCGGAGTTGATGGATACAGAACTATACATGCCTATCTTATTCGTAAAGGATACGATATTAGCCGCT
TAACAGTTCACAAATATATGAATACTGAAATGCAGTTGTTTTCAATTTCAAGAAAAAAGAAAACAACATATGAACATGGCGTCGCTCACAAAGTATACGA
GAACAAACTGAATCAGAATTTTCGAGCAGATGAAATCAATCACAAGTGGTGTACAGATTTTACTTATCTTTTCCTGACGGATGGCAGCAAGCGTTATAAT
TGCACGATTATAGATCTACATGACCGAAGCGTTATTGCAAGTATAACGGACAGAAATATAACCGCTGATTTAGCGAAAAGAACGTTGGAAAAAGCAATTC
ATTCTCAACCAGGAATTGACTTGAGCAAGCTTCTCGTGCATTCGGATCAAGGAAGCCAGTACACATCAAAAGAGTTCACTGAATTTTGTGAGGAGCTTGG
CATCACTCAAAGTATGAGTAAGGCTGGATATCCATATGATAATGCTCCTATGGAAAGATATTTTAATACATTGAAAAATGATCTTATTTACCAGCATTAT
TATCGTACAGAGGAAGAACTTTACACAGCAATCGAAGAATTTGCGTATGTACAATATAATCATGTACGACCGCATTCTTATAATAACTACAAAACGCCTT
ATGAGGCACGCTACGGGAGTGTATAACTCCTGTAGTGGAAATTAGGTCGTAGTGTTACAAAAAAGCTTGACCACAACA
TCAAGAAGAAGATAGTCCGTCTTCATCTTGAAGAGGGAAGATCCCTCAAAGGTCTTGCTGAAGAATATGGTGTATCCAAAGCAAGTATATCTATTTGGAC
AAAACAATTCCGTGAAGAATGCCAAACAAACGACGAAGCCAAAGCCGATTATGATTACATGAAAGAGAATCTACAGCTTAAAAAGCAACTTGCAGAACTC
CAAAAGGAAAATGACTTCTTAAAAAAAGCAGCGGCATTCTTTGCGAAGGAAATCGATTAGAGGCTTATCGATTCATTCAGAAATACAACAAAGACTTTGG
ACTCAGATGGCTTCTTAGAAAGTTTAACATCTGTCCAAATGCTTATTACAATTATCTAAAAAATCGAAAAGCTGATTATCATCAACAGAAAGATGAGATC
AAAGATTCCATTCGAGAAATCTATCATTCTCATGGCGGAGTTGATGGATACAGAACTATACATGCCTATCTTATTCGTAAAGGATACGATATTAGCCGCT
TAACAGTTCACAAATATATGAATACTGAAATGCAGTTGTTTTCAATTTCAAGAAAAAAGAAAACAACATATGAACATGGCGTCGCTCACAAAGTATACGA
GAACAAACTGAATCAGAATTTTCGAGCAGATGAAATCAATCACAAGTGGTGTACAGATTTTACTTATCTTTTCCTGACGGATGGCAGCAAGCGTTATAAT
TGCACGATTATAGATCTACATGACCGAAGCGTTATTGCAAGTATAACGGACAGAAATATAACCGCTGATTTAGCGAAAAGAACGTTGGAAAAAGCAATTC
ATTCTCAACCAGGAATTGACTTGAGCAAGCTTCTCGTGCATTCGGATCAAGGAAGCCAGTACACATCAAAAGAGTTCACTGAATTTTGTGAGGAGCTTGG
CATCACTCAAAGTATGAGTAAGGCTGGATATCCATATGATAATGCTCCTATGGAAAGATATTTTAATACATTGAAAAATGATCTTATTTACCAGCATTAT
TATCGTACAGAGGAAGAACTTTACACAGCAATCGAAGAATTTGCGTATGTACAATATAATCATGTACGACCGCATTCTTATAATAACTACAAAACGCCTT
ATGAGGCACGCTACGGGAGTGTATAACTCCTGTAGTGGAAATTAGGTCGTAGTGTTACAAAAAAGCTTGACCACAACA
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 | |
|---|---|---|---|---|---|
| 294 bp | 97 aa | 67 | 360 | + | No |
Description : First part of the transposase
ORF sequence :
MLKMSQYYDPEFKKKIVRLHLEEGRSLKGLAEEYGVSKASISIWTKQFREECQTNDEAKADYDYMKENLQLKKQLAELQKENDFLKKAAAFFAKEID
Blast result :ORF 2
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 912 bp | 303 aa | 315 | 1226 | + | No |
Description : Second part of the transposase
ORF sequence :
LLKKSSGILCEGNRLEAYRFIQKYNKDFGLRWLLRKFNICPNAYYNYLKNRKADYHQQKDEIKDSIREIYHSHGGVDGYRTIHAYLIRKGYDISRLTVHK
YMNTEMQLFSISRKKKTTYEHGVAHKVYENKLNQNFRADEINHKWCTDFTYLFLTDGSKRYNCTIIDLHDRSVIASITDRNITADLAKRTLEKAIHSQPG
IDLSKLLVHSDQGSQYTSKEFTEFCEELGITQSMSKAGYPYDNAPMERYFNTLKNDLIYQHYYRTEEELYTAIEEFAYVQYNHVRPHSYNNYKTPYEARY
GSV
YMNTEMQLFSISRKKKTTYEHGVAHKVYENKLNQNFRADEINHKWCTDFTYLFLTDGSKRYNCTIIDLHDRSVIASITDRNITADLAKRTLEKAIHSQPG
IDLSKLLVHSDQGSQYTSKEFTEFCEELGITQSMSKAGYPYDNAPMERYFNTLKNDLIYQHYYRTEEELYTAIEEFAYVQYNHVRPHSYNNYKTPYEARY
GSV
Blast result :ORF 3
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1160 bp | 386 aa | 67 | 1226 | + | Yes |
Chemistry : DDE
ORF sequence :
MLKMSQYYDPEFKKKIVRLHLEEGRSLKGLAEEYGVSKASISIWTKQFREECQTNDEAKADYDYMKENLQLKKQLAELQKENDFLKKSSGILCEGNRLEA
YRFIQKYNKDFGLRWLLRKFNICPNAYYNYLKNRKADYHQQKDEIKDSIREIYHSHGGVDGYRTIHAYLIRKGYDISRLTVHKYMNTEMQLFSISRKKKT
TYEHGVAHKVYENKLNQNFRADEINHKWCTDFTYLFLTDGSKRYNCTIIDLHDRSVIASITDRNITADLAKRTLEKAIHSQPGIDLSKLLVHSDQGSQYT
SKEFTEFCEELGITQSMSKAGYPYDNAPMERYFNTLKNDLIYQHYYRTEEELYTAIEEFAYVQYNHVRPHSYNNYKTPYEARYGSV
YRFIQKYNKDFGLRWLLRKFNICPNAYYNYLKNRKADYHQQKDEIKDSIREIYHSHGGVDGYRTIHAYLIRKGYDISRLTVHKYMNTEMQLFSISRKKKT
TYEHGVAHKVYENKLNQNFRADEINHKWCTDFTYLFLTDGSKRYNCTIIDLHDRSVIASITDRNITADLAKRTLEKAIHSQPGIDLSKLLVHSDQGSQYT
SKEFTEFCEELGITQSMSKAGYPYDNAPMERYFNTLKNDLIYQHYYRTEEELYTAIEEFAYVQYNHVRPHSYNNYKTPYEARYGSV
Blast result :
Comments
ISRgn1 is 56% aa similar to IS1163 for ORF1 and 46% aa similar to IS1069 for ORF2. There is a potential frameshift motif at position 321-327.
ISRgn1 has been identified in the genome of Ruminococcus gnavus E1, a Gram-positive, strict-anaerobic strain isolated from a human intestinal flora.
ISRgn1 is present in two copies in the E1 strain. Furthermore, two additional copies were found in two independent isolates of E1 strain, suggesting that the IS is functional.
The distribution of ISRgn1 among 21 strains belonging to the same phylogenetic cluster than E1 and isolated from different intestinal floras revealed that it is present in a single copy in only one strain, R. gnavus B53.
This observation, together with the discrepancy between the GC content of the insertion element and the E1 chromosome (36% vs 43%) could indicate that ISRgn1 is not native to R. gnavus.
ISRgn1 has been identified in the genome of Ruminococcus gnavus E1, a Gram-positive, strict-anaerobic strain isolated from a human intestinal flora.
ISRgn1 is present in two copies in the E1 strain. Furthermore, two additional copies were found in two independent isolates of E1 strain, suggesting that the IS is functional.
The distribution of ISRgn1 among 21 strains belonging to the same phylogenetic cluster than E1 and isolated from different intestinal floras revealed that it is present in a single copy in only one strain, R. gnavus B53.
This observation, together with the discrepancy between the GC content of the insertion element and the E1 chromosome (36% vs 43%) could indicate that ISRgn1 is not native to R. gnavus.
References
1] Gomez-Rodriguez,A., Ladire,M., Marcille,F. and Fons,M. (2001) Direct submission GenBank.