ISRel6

  • Family IS630
  • Group
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
NC_004041 ND Rhizobium etli
Rhizobium etli CFN 42 symbiotic plasmid p42d
Rhizobium etli CFN 42 plasmid p42b
Rhizobium etli CFN 42
DNA section
IS Length : 1047 bp

Ends


IR Length : 18/26

IRL : GAGCGGATCATTTCTTATCGGAATCGGTGCGGGATTCCCAAATCAGCAGA
IRR : GAGCCTTTCATGTTTTGACGGAAGCGTAGCCAGCATTTGAGAAGTAGTTG

Insertion site


Left flankDirect repeatRight flankDR Length
GGACTTGCTCTAGGTCGCTCGT2
AATGAAACGCTAGCGTAACGAT2
CGCCAACTGCTAGGCATCGTCT2
CGCATTGCGTTAGCCCCTCCCC2
CTGGCTTCCTTAGGCGGCACGC2

DNA sequence

GAGCGGATCATTTCTTATCGGAATCGGTGCGGGATTCCCAAATCAGCAGATTTGTGATTCATGATGGATGCTGGAATGGAGGCCAGCATCCATGACGCGA
CCCTATTCGAATGATCTTCGCGAGCGAGTCATTGCAGCGGTTGTGGACGGTCAGAGCTGCCGGGTGGTGGCGGAGCGGTTCAACATAGCTATCTCATCCG
TGGTGAAGTGGTCGCAGCGTTATCGGGCCACCGGTAGTGTGTCGCCCGGTAAGATGGGCGGCCATCGCCGACGTGTGCTGGAGCCGCACCGCGCCTTCAT
TGTCGAGCAGATCGAGCAGACATCACATCTGACGCTACATCGGCTGAAGGATGAGTTAGCCGCCCGCGGTGTGAGCGTCTCCCACAATGCCATCTGGCAA
TTCATGCGCCGCGAGGGCTTGAGCTTTAAAAAAAACGCTGTTCGCCCTTGAGCAGGGCCGCGCCGACATTGCCCGCCGCAGAGCTCGCTGGAAAGCCTGG
CAAGACCGCTTCGATCCGAAGCGGCTCGTCTTTATTGACGAGACCTGGATCCGCACCAACATGGCGCCGTTACGCGGCTGGGGGCCGAGGGGCAAAAGAT
TACGCGGCTTTGCCCCGCATGGCCGCTGGCGCACCCTCACCTTCCTCGGCGCCCTACGCTGCGACAAGCTCACTGCACCCTGCGTCTTCGACGGTCCCAT
CAATGGCGAATGCTTTCACGCCTATGTCCGCCAGCAGTTGATCCCGACCCTCAAACCTGGCGACATCGTCATCCTCGATAATCTCGGCTCTCACAAAGCC
AAGGCCATCCGCGATGCCATCAGGGCCGTCGGCGCCAGGCTCTGGTTCCTGCCGAAATATTCCCCCGACCTTAACCCGATCGAGCAGGCCTTCGCCAAGA
TCAAGCACTGGATGCGCCAGGCCCAAAAGCGAACCATCGAGGAAACCTGGCGCTATCTGGGCATACTCGCCGACACTATCAAGCCAGAGGAATGCGCCAA
CTACTTCTCAAATGCTGGCTACGCTTCCGTCAAAACATGAAAGGCTC
Recoding section
  • Recoding by frameshift
  • Frame
  • Type
  • Experimentally demonstrated

Stimulators :

  • Shine-Dalgarno sequence :
  • Secondary structure :

Recoding motif :

Protein section
ORF number : 3

 

ORF 1
LengthBeginEndStrandFusion ORF
360 bp119 aa92451+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MTRPYSNDLRERVIAAVVDGQSCRVVAERFNIAISSVVKWSQRYRATGSVSPGKMGGHRRRVLEPHRAFIVEQIEQTSHLTLHRLKDELAARGVSVSHNA
IWQFMRREGLSFKKNAVRP

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
618 bp205 aa4231040+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

ALKKTLFALEQGRADIARRRARWKAWQDRFDPKRLVFIDETWIRTNMAPLRGWGPRGKRLRGFAPHGRWRTLTFLGALRCDKLTAPCVFDGPINGECFHA
YVRQQLIPTLKPGDIVILDNLGSHKAKAIRDAIRAVGARLWFLPKYSPDLNPIEQAFAKIKHWMRQAQKRTIEETWRYLGILADTIKPEECANYFSNAGY
ASVKT

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
949 bp315 aa921040+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MTRPYSNDLRERVIAAVVDGQSCRVVAERFNIAISSVVKWSQRYRATGSVSPGKMGGHRRRVLEPHRAFIVEQIEQTSHLTLHRLKDELAARGVSVSHNA
IWQFMRREGLSFKKTLFALEQGRADIARRRARWKAWQDRFDPKRLVFIDETWIRTNMAPLRGWGPRGKRLRGFAPHGRWRTLTFLGALRCDKLTAPCVFD
GPINGECFHAYVRQQLIPTLKPGDIVILDNLGSHKAKAIRDAIRAVGARLWFLPKYSPDLNPIEQAFAKIKHWMRQAQKRTIEETWRYLGILADTIKPEE
CANYFSNAGYASVKT

 

Blast result :
Comments
ISRle6 is 71% aa similar to ISGdi6.
The third ORF is a putative ORFAB transposase reconstructed in silico by a possible +1 frameshift.
References
1] Lozano LF. (2010) Direct submission.

2] González V, Santamaría RI, Bustos P, Hernández-González I, Medrano-Soto A, Moreno-Hagelsieb G, Janga SC, Ramírez MA, Jiménez-Jacinto V, Collado-Vides J, Dávila G. (2006) PNAS. 7;103(10):3834-9

3] Gonzalez V, Bustos P, Ramirez-Romero M.A, Medrano-Soto A, Salgado H, Hernandez-Gonzalez I, Hernandez-Celis JC, Quintero V, Moreno-Hagelsieb G, Girard L, Rodriguez O, Flores M, Cevallos MA, Collado-Vides J, Romero D, and Davila G. (2003) Genome Biol. 4 (6), R36

4] Quintero V, Cevallos MA, and Davila G. (2002) Mol. Microbiol. 46 (4), 1023-1032

5] Ramirez-Romero MA, Bustos P, Girard L, Rodriguez O, Cevallos MA, and Davila G. (1997) Microbiology (Reading, Engl.) 143 (PT 8), 2825-2831

6] Girard ML, Flores M, Brom S, Romero D, Palacios R, and Davila G. (1991) J. Bacteriol. 173 (8), 2411-2419