ISRm1
- Family IS3
- Group IS2
Isoform Synonym(s) ISpRm20111, ISpRmUSDA1024-2, ISpRm1
| Accession number | Transposition | Origin | Host |
|---|---|---|---|
| X56563 | Y | Rhizobium meliloti | Rhizobium meliloti USDA1024 Rhizobium meliloti IZ450 Rhizobium meliloti ATCC9930 Rhizobium meliloti DMG117 Rhizobium meliloti JJ1c10 plasmid pRmeJJ1c10a Rhizobium meliloti 1021 plasmid pRmeSU47a Bradyrhizobium sp. 191 Rhizobium leguminosarum biovar phaseoli CFN-Rph215 Rhizobium meliloti 1021 plasmid pRmeSU47b Rhizobium meliloti 102F34 Rhizobium meliloti NRG185 Rhizobium meliloti R304 Rhizobium meliloti SU47 Rhizobium meliloti 2011 |
DNA section
IS Length : 1319 bp
Ends
IR Length : 25/32
IRL : TGAATTAGCCCCCGAAAGGTCCGGACGTGCTCCCCCACTTAGCTAAGTGG
IRR : TGGAGTTGCCCCCAAAAGACCGGACATGCTCAGGTTTGAGATTGCGAACT
Insertion site
| Left flank | Direct repeat | Right flank | DR Length |
|---|---|---|---|
| GTCGCTATTG | GACAA | TGTACACAAC | 5 |
| ATAATGGTCA | TGCAC | GCAATAATCA | 5 |
| ACAACGCACG | ATCTG | ATCATAAGCA | 5 |
| GGCGCGACTT | GGGAG | AGGGTGAACG | 5 |
DNA sequence
TGAATTAGCCCCCGAAAGGTCCGGACGTGCTCCCCCACTTAGCTAAGTGGGTAGGAGTAATGTTGGTAATATGACTAGCAGCAATTTTAAGATGGAAGTT
CTCTCCGGGCCGGAACGTCGGCGGCGCTGGAGCACGGCAGAGAAGCTGGCGATCATCCACGAGACCTATGAGGCGGACGCGACGGTGAGCATCGTCGCGC
GTCGGCACGGCATTCAGCCGAACCAGTTGTTCGCCTGGCGCAAGCTGGCGTCCCAAGGGGCACTGACGGCGACGGCCGCCGAAGAGGAGGTCGTTCCGGC
TTCCGAATACCGGGCGCTTCAGGCGCAGGTGAAGGAGTTGCAACGCCTGTTGGGCAAGAAGACGATGGAGAGCGAAATCCTGAAGGAAGCCCTCGAAATC
GCCGGTAGCCCAAAAAAACATCTGTTGCGCTCGCTCTCTCTTCCGAGGGGGATTTTGGGATGAAGACCGTTTGCGAAACTTTGGGTGTCGCTCGCTCGAA
TATCGCCGCGCGTGCCGCAGGCTCCCCTTCCAGAGCCAGAGGACGCCCGCCACTACCTGATCGCGAGCTGGTGGAGGACATCAAGGCCGTCATCGCCGAT
ATGCCCACCTACGGCTATCGGCGTGTCCATGCCATCCTGCGTCGGAATGCCCGGAAACTGGGGCGTTCGTGGCCCAATGCCAAGCGCGTCTACCGGGTGA
TGAAGCTGCACAATCTGCTATTGGTGCGCCACACCGGAGCGGTCGATGATCGTCTCCACGAGGGTCAGGTCGCTGTCGAACGTTCGAACATCAGATGGTG
CTCCGACGGCTTCGAGATCGGCTGCGACAACAAGGAGAAGGTCCGGGTCGCCTTCGCCCTCGACTGCTGCGACCGTGAAGCAATCGCCCATGTCGCCACC
ACCGAGGGCATCAAGAGCCAGGACGTGCAGGACCTCGTGATCACAGCAGTGGAGAACCGCTTCGGCCGCATCAACATGCTGTCCGAGCCCATCGAATGGC
TCACCGACAACGGCTCCTGCTTCATCGCCAAGGACACCGCATCCTTGCTCCGCGACATCGGCATGGAACCTTGCACGACACCGGTGCGAAGCCCACAGTC
GAACGGCATGGCCGAGGCGTTCGTGAAAACATTCAAGCGCGATTACGTCTCGGTGAACCCAACCCCCGACGCTGAAACCGTCATGGCGCAACTGCCGTTC
TGGTTCGAGCATTACAACAATCTTCACCCGCACAGTGCTTTAGGATATCAATCGCCGCGCGAGTTCATCAGTTCGCAATCTCAAACCTGAGCATGTCCGG
TCTTTTGGGGGCAACTCCA
CTCTCCGGGCCGGAACGTCGGCGGCGCTGGAGCACGGCAGAGAAGCTGGCGATCATCCACGAGACCTATGAGGCGGACGCGACGGTGAGCATCGTCGCGC
GTCGGCACGGCATTCAGCCGAACCAGTTGTTCGCCTGGCGCAAGCTGGCGTCCCAAGGGGCACTGACGGCGACGGCCGCCGAAGAGGAGGTCGTTCCGGC
TTCCGAATACCGGGCGCTTCAGGCGCAGGTGAAGGAGTTGCAACGCCTGTTGGGCAAGAAGACGATGGAGAGCGAAATCCTGAAGGAAGCCCTCGAAATC
GCCGGTAGCCCAAAAAAACATCTGTTGCGCTCGCTCTCTCTTCCGAGGGGGATTTTGGGATGAAGACCGTTTGCGAAACTTTGGGTGTCGCTCGCTCGAA
TATCGCCGCGCGTGCCGCAGGCTCCCCTTCCAGAGCCAGAGGACGCCCGCCACTACCTGATCGCGAGCTGGTGGAGGACATCAAGGCCGTCATCGCCGAT
ATGCCCACCTACGGCTATCGGCGTGTCCATGCCATCCTGCGTCGGAATGCCCGGAAACTGGGGCGTTCGTGGCCCAATGCCAAGCGCGTCTACCGGGTGA
TGAAGCTGCACAATCTGCTATTGGTGCGCCACACCGGAGCGGTCGATGATCGTCTCCACGAGGGTCAGGTCGCTGTCGAACGTTCGAACATCAGATGGTG
CTCCGACGGCTTCGAGATCGGCTGCGACAACAAGGAGAAGGTCCGGGTCGCCTTCGCCCTCGACTGCTGCGACCGTGAAGCAATCGCCCATGTCGCCACC
ACCGAGGGCATCAAGAGCCAGGACGTGCAGGACCTCGTGATCACAGCAGTGGAGAACCGCTTCGGCCGCATCAACATGCTGTCCGAGCCCATCGAATGGC
TCACCGACAACGGCTCCTGCTTCATCGCCAAGGACACCGCATCCTTGCTCCGCGACATCGGCATGGAACCTTGCACGACACCGGTGCGAAGCCCACAGTC
GAACGGCATGGCCGAGGCGTTCGTGAAAACATTCAAGCGCGATTACGTCTCGGTGAACCCAACCCCCGACGCTGAAACCGTCATGGCGCAACTGCCGTTC
TGGTTCGAGCATTACAACAATCTTCACCCGCACAGTGCTTTAGGATATCAATCGCCGCGCGAGTTCATCAGTTCGCAATCTCAAACCTGAGCATGTCCGG
TCTTTTGGGGGCAACTCCA
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 | |
|---|---|---|---|---|---|
| 393 bp | 130 aa | 71 | 463 | + | No |
Description : First part of the transposase
ORF sequence :
MTSSNFKMEVLSGPERRRRWSTAEKLAIIHETYEADATVSIVARRHGIQPNQLFAWRKLASQGALTATAAEEEVVPASEYRALQAQVKELQRLLGKKTME
SEILKEALEIAGSPKKHLLRSLSLPRGILG
SEILKEALEIAGSPKKHLLRSLSLPRGILG
Blast result :ORF 2
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 882 bp | 293 aa | 409 | 1290 | + | No |
Description : Second part of the transposase
ORF sequence :
PKKTSVALALSSEGDFGMKTVCETLGVARSNIAARAAGSPSRARGRPPLPDRELVEDIKAVIADMPTYGYRRVHAILRRNARKLGRSWPNAKRVYRVMKL
HNLLLVRHTGAVDDRLHEGQVAVERSNIRWCSDGFEIGCDNKEKVRVAFALDCCDREAIAHVATTEGIKSQDVQDLVITAVENRFGRINMLSEPIEWLTD
NGSCFIAKDTASLLRDIGMEPCTTPVRSPQSNGMAEAFVKTFKRDYVSVNPTPDAETVMAQLPFWFEHYNNLHPHSALGYQSPREFISSQSQT
HNLLLVRHTGAVDDRLHEGQVAVERSNIRWCSDGFEIGCDNKEKVRVAFALDCCDREAIAHVATTEGIKSQDVQDLVITAVENRFGRINMLSEPIEWLTD
NGSCFIAKDTASLLRDIGMEPCTTPVRSPQSNGMAEAFVKTFKRDYVSVNPTPDAETVMAQLPFWFEHYNNLHPHSALGYQSPREFISSQSQT
Blast result :ORF 3
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1220 bp | 406 aa | 71 | 1290 | + | Yes |
Chemistry : DDE
ORF sequence :
MTSSNFKMEVLSGPERRRRWSTAEKLAIIHETYEADATVSIVARRHGIQPNQLFAWRKLASQGALTATAAEEEVVPASEYRALQAQVKELQRLLGKKTME
SEILKEALEIAGSPKKTSVALALSSEGDFGMKTVCETLGVARSNIAARAAGSPSRARGRPPLPDRELVEDIKAVIADMPTYGYRRVHAILRRNARKLGRS
WPNAKRVYRVMKLHNLLLVRHTGAVDDRLHEGQVAVERSNIRWCSDGFEIGCDNKEKVRVAFALDCCDREAIAHVATTEGIKSQDVQDLVITAVENRFGR
INMLSEPIEWLTDNGSCFIAKDTASLLRDIGMEPCTTPVRSPQSNGMAEAFVKTFKRDYVSVNPTPDAETVMAQLPFWFEHYNNLHPHSALGYQSPREFI
SSQSQT
SEILKEALEIAGSPKKTSVALALSSEGDFGMKTVCETLGVARSNIAARAAGSPSRARGRPPLPDRELVEDIKAVIADMPTYGYRRVHAILRRNARKLGRS
WPNAKRVYRVMKLHNLLLVRHTGAVDDRLHEGQVAVERSNIRWCSDGFEIGCDNKEKVRVAFALDCCDREAIAHVATTEGIKSQDVQDLVITAVENRFGR
INMLSEPIEWLTDNGSCFIAKDTASLLRDIGMEPCTTPVRSPQSNGMAEAFVKTFKRDYVSVNPTPDAETVMAQLPFWFEHYNNLHPHSALGYQSPREFI
SSQSQT
Blast result :
Comments
ISRm1 transposes (preferentially, in the case of strain 1021) into the nitrogen fixation genes (nifHDK/fix), but also into the nodulation genes (nodDABC) (Ruvkun et al., 1982). However, it does not apparently affect symbiotic or competitive properties of Rhizobium meliloti (Barran et al., 1991). ISRm1 is possibly identical to ISpRm1 (Simon et al., 1991). ISRm1 is 55 and 54 % homologous to IS2 and IS426, respectively.
September 21 2012 : the file of ISpRm1 (partial sequence) was deleted and information added to the file of ISRm1 (isoforme).
Previous comments in ISpRm1 file : Promotes transcription of adjacent genes. ISpRm1 is closely related (maybe identical) to ISRm1, based on restriction mapping and hybridization experiments (Labes and Simon, 1990; Simon et al., 1991).
September 21 2012 : the file of ISpRm1 (partial sequence) was deleted and information added to the file of ISRm1 (isoforme).
Previous comments in ISpRm1 file : Promotes transcription of adjacent genes. ISpRm1 is closely related (maybe identical) to ISRm1, based on restriction mapping and hybridization experiments (Labes and Simon, 1990; Simon et al., 1991).
References