ISDsh1
- Family IS3
- Group IS51
Isoform Synonym(s)
| Accession number | Transposition | Origin | Host |
|---|---|---|---|
| NZ_AAVE01000008 | ND | Dinoroseobacter shibae | Dinoroseobacter shibae DFL 12 |
DNA section
IS Length : 1326 bp
Ends
IR Length : 31 /42
IRL : TGAATCGCCCCGAGTTTGTCGGAGACCATCAACTTAAGTAAGGATGATGG
IRR : TGAATCGCCCCGGTTTTACCGGAGACCTATAGCTTCATTTCACGCGACCA
Insertion site
| Left flank | Direct repeat | Right flank | DR Length |
|---|---|---|---|
| CTCCTTGAGG | ATG | CGGTTCTCAC | 3 |
DNA sequence
TGAATCGCCCCGAGTTTGTCGGAGACCATCAACTTAAGTAAGGATGATGGTTATGACAAAAAGCAAAATGGCAAATCGCTACTCGCCAGAGGTCCGCGCG
CGTGCGGTCCGGATGGTGTTCGAGCATCAAGGTTCCTACGAAACGCAGGCGGGCGCGATAGCGGCCATCGCACCCAAGATCGGCTGCATTCCCCAGACTT
TGCGCGAATGGGTCAAACAGGCTGAGAAGGACAGCGGCATCCGTGATGGCGTGACAACCGAGGAACGCGACCGGATCAAGACCCTCGAACGCGAGAACCG
GGAACTGCGCCAGGCGAACGAGATCCTGCGCAAGGCATCAGCTTATTTTGCGCAGGCGGAACTCGACCGCCCACTGAAGCGATGATCGCCTTCATTGAGG
ATCAGCGCGTTGTTTACGGTGTCGAGTCGATCTGCAGGGTGCTGCCGATCGCGCCGTCAACATTCTATCACCACCTGGCGTGCCTCGCTGATCCGTCCAA
AGCTTCGGCCCGGCATCAGCGGGATACGGAGCTGCGCCCGGAGATCAAACGTGTCTGGGATGAGAATTATCAGGTCTACGGGGTCCGTAAGGCATGGCAT
CAGCTGAAGCGCGAGGGCTTTGAGCTGGCGCGCTGCACGGTGGAGCGGCTGATGAAACATATCGGCATCCGTGGGGCTGTGCGCGGCAAGGTGGTCAAAA
CAACCGTCCCTGACACGTCAGCGCCTTGTCCGCGTGACAAGGTGAACCGCGTGTTCCGGGCACCAGCCCCGAACCTCCTCTGGGTCAGCGATTTTACCTA
CGTGTCGACATGGCAGGGCTTTGTCTATGTTGCCTTCGTCATCGACACGTTTGCAGATCGCATCGTCGGCTGGCGGGTCTCACGGTCGGCCAAAACAGAC
TTTGTTCTCGATGCTCTTGAACAGGCCCTGCATGATCGACGGCCGGTCCAAAAGAGCGGCTTGGTCCACCACTCGGATCGTGGCGGGCAATATTTATCCA
TTCGCTATACCGAGCGTCTGGCCGAAGCTGGCATCGAGCCATCGGTCGGCAGCGTCGGGGATTCCTATGACAACGCCCTCGCAGAAACGATCAATGGTCT
ATACAAAACCGAGCTGGTCCATCGTCAAGGACCGTGGCGCAATATGCAGGATCTGGAAATGGCGACACTCGGCTGGGTCGATTGGTTCAACAACCGGCGC
CTGCTTGGACCCATCGGAAACATCCCGCCAGCAGAGGCTGAAGACAACTTCTATGCATACCGCGAAGTGCTCGATATGGTCGCGTGAAATGAAGCTATAG
GTCTCCGGTAAAACCGGGGCGATTCA
CGTGCGGTCCGGATGGTGTTCGAGCATCAAGGTTCCTACGAAACGCAGGCGGGCGCGATAGCGGCCATCGCACCCAAGATCGGCTGCATTCCCCAGACTT
TGCGCGAATGGGTCAAACAGGCTGAGAAGGACAGCGGCATCCGTGATGGCGTGACAACCGAGGAACGCGACCGGATCAAGACCCTCGAACGCGAGAACCG
GGAACTGCGCCAGGCGAACGAGATCCTGCGCAAGGCATCAGCTTATTTTGCGCAGGCGGAACTCGACCGCCCACTGAAGCGATGATCGCCTTCATTGAGG
ATCAGCGCGTTGTTTACGGTGTCGAGTCGATCTGCAGGGTGCTGCCGATCGCGCCGTCAACATTCTATCACCACCTGGCGTGCCTCGCTGATCCGTCCAA
AGCTTCGGCCCGGCATCAGCGGGATACGGAGCTGCGCCCGGAGATCAAACGTGTCTGGGATGAGAATTATCAGGTCTACGGGGTCCGTAAGGCATGGCAT
CAGCTGAAGCGCGAGGGCTTTGAGCTGGCGCGCTGCACGGTGGAGCGGCTGATGAAACATATCGGCATCCGTGGGGCTGTGCGCGGCAAGGTGGTCAAAA
CAACCGTCCCTGACACGTCAGCGCCTTGTCCGCGTGACAAGGTGAACCGCGTGTTCCGGGCACCAGCCCCGAACCTCCTCTGGGTCAGCGATTTTACCTA
CGTGTCGACATGGCAGGGCTTTGTCTATGTTGCCTTCGTCATCGACACGTTTGCAGATCGCATCGTCGGCTGGCGGGTCTCACGGTCGGCCAAAACAGAC
TTTGTTCTCGATGCTCTTGAACAGGCCCTGCATGATCGACGGCCGGTCCAAAAGAGCGGCTTGGTCCACCACTCGGATCGTGGCGGGCAATATTTATCCA
TTCGCTATACCGAGCGTCTGGCCGAAGCTGGCATCGAGCCATCGGTCGGCAGCGTCGGGGATTCCTATGACAACGCCCTCGCAGAAACGATCAATGGTCT
ATACAAAACCGAGCTGGTCCATCGTCAAGGACCGTGGCGCAATATGCAGGATCTGGAAATGGCGACACTCGGCTGGGTCGATTGGTTCAACAACCGGCGC
CTGCTTGGACCCATCGGAAACATCCCGCCAGCAGAGGCTGAAGACAACTTCTATGCATACCGCGAAGTGCTCGATATGGTCGCGTGAAATGAAGCTATAG
GTCTCCGGTAAAACCGGGGCGATTCA
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 | |
|---|---|---|---|---|---|
| 333 bp | 110 aa | 53 | 385 | + | No |
Description : First part of the transposase
ORF sequence :
MTKSKMANRYSPEVRARAVRMVFEHQGSYETQAGAIAAIAPKIGCIPQTLREWVKQAEKDSGIRDGVTTEERDRIKTLERENRELRQANEILRKASAYFA
QAELDRPLKR
QAELDRPLKR
Blast result :ORF 2
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1041 bp | 346 aa | 247 | 1287 | + | No |
Description : Second part of the transposase
ORF sequence :
WRDNRGTRPDQDPRTREPGTAPGERDPAQGISLFCAGGTRPPTEAMIAFIEDQRVVYGVESICRVLPIAPSTFYHHLACLADPSKASARHQRDTELRPEI
KRVWDENYQVYGVRKAWHQLKREGFELARCTVERLMKHIGIRGAVRGKVVKTTVPDTSAPCPRDKVNRVFRAPAPNLLWVSDFTYVSTWQGFVYVAFVID
TFADRIVGWRVSRSAKTDFVLDALEQALHDRRPVQKSGLVHHSDRGGQYLSIRYTERLAEAGIEPSVGSVGDSYDNALAETINGLYKTELVHRQGPWRNM
QDLEMATLGWVDWFNNRRLLGPIGNIPPAEAEDNFYAYREVLDMVA
KRVWDENYQVYGVRKAWHQLKREGFELARCTVERLMKHIGIRGAVRGKVVKTTVPDTSAPCPRDKVNRVFRAPAPNLLWVSDFTYVSTWQGFVYVAFVID
TFADRIVGWRVSRSAKTDFVLDALEQALHDRRPVQKSGLVHHSDRGGQYLSIRYTERLAEAGIEPSVGSVGDSYDNALAETINGLYKTELVHRQGPWRNM
QDLEMATLGWVDWFNNRRLLGPIGNIPPAEAEDNFYAYREVLDMVA
Blast result :ORF 3
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1235 bp | 411 aa | 53 | 1287 | + | Yes |
Chemistry : DDE
ORF sequence :
MTKSKMANRYSPEVRARAVRMVFEHQGSYETQAGAIAAIAPKIGCIPQTLREWVKQAEKDSGIRDGVTTEERDRIKTLERENRELRQANEILRKASAYFC
AGGTRPPTEAMIAFIEDQRVVYGVESICRVLPIAPSTFYHHLACLADPSKASARHQRDTELRPEIKRVWDENYQVYGVRKAWHQLKREGFELARCTVERL
MKHIGIRGAVRGKVVKTTVPDTSAPCPRDKVNRVFRAPAPNLLWVSDFTYVSTWQGFVYVAFVIDTFADRIVGWRVSRSAKTDFVLDALEQALHDRRPVQ
KSGLVHHSDRGGQYLSIRYTERLAEAGIEPSVGSVGDSYDNALAETINGLYKTELVHRQGPWRNMQDLEMATLGWVDWFNNRRLLGPIGNIPPAEAEDNF
YAYREVLDMVA
AGGTRPPTEAMIAFIEDQRVVYGVESICRVLPIAPSTFYHHLACLADPSKASARHQRDTELRPEIKRVWDENYQVYGVRKAWHQLKREGFELARCTVERL
MKHIGIRGAVRGKVVKTTVPDTSAPCPRDKVNRVFRAPAPNLLWVSDFTYVSTWQGFVYVAFVIDTFADRIVGWRVSRSAKTDFVLDALEQALHDRRPVQ
KSGLVHHSDRGGQYLSIRYTERLAEAGIEPSVGSVGDSYDNALAETINGLYKTELVHRQGPWRNMQDLEMATLGWVDWFNNRRLLGPIGNIPPAEAEDNF
YAYREVLDMVA
Blast result :
Comments
ISDsh1 is 84 % (ORFA) aa similar to IS51 and 83% (ORFB) aa similar to ISRtr2 . The third ORF is a putative ORFAB transposase reconstructed in sillico by possible -1 frameshift.
Genome in progress.
Genome in progress.
References
1] Copeland,A., Lucas,S., Lapidus,A., Barry,K., Glavina del Rio,T., Dalin,E., Tice,H., Bruce,D., Pitluck,S. and Richardson,P. US DOE Joint Genome Institute (2006) Direct submission GenBank.