ISPmar2

  • Family IS3
  • Group IS407
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
GU997096 Y Paracoccus marcusii
Paracoccus marcusii DSM 11574
DNA section
IS Length : 1269 bp

Ends


IR Length : 18/25

IRL : TGGTCTGCCCCCTGAAAAGTGGTCCTCCCTAAGGTATGGCTTTTGAGCCA
IRR : TGGCCTGCCCCTATCGGGTGGTCCGGTTTCAGTCTTAGTGCATTACGGGT

Insertion site


Left flankDirect repeatRight flankDR Length
TGGCTTGGAGCCTGTTGGTGCGGT4

DNA sequence

TGGTCTGCCCCCTGAAAAGTGGTCCTCCCTAAGGTATGGCTTTTGAGCCATTTGGAGGATGCAGGAATGCCCCAGAAAAAGCACAAGCCGGAAGAGATCG
TCGCCAAGCTCCGGCAGGTTGACGTGTTGGTGTCGCAAGGCCAGTCGGTGGCCGAAGCCGTGCGGTCGATCAGCGTGACGCAGTTCACCTACTATCGGTG
GCGCAAGGAGTTCGGTGGGCTGAAAACCGACCAAGTGAAGCGATTGAAGGAGCTGGAGAAGGAGAATGAGCGGCTCCGGAAGGCCGTCTCTGACCTGACG
CTCGAGAAGCTCATCCTTCGGGAAGCGGCATCGGGAAACTTCTGAGCCCCGCCCGCCGCCGTGCTTGCATCGAGCATGTCAGGCAGAAGTTCCGGATCTC
GGAACGGCTCGCCTGTCGCGTGCTCGGGCAGCATCGCTCGACACAGCGGAAAGTGCCGAGTGGACGGGCCGATGAAAACGTCCTGACGGCCGACATCATC
GCGCTCGCCTCGCAATATGGGCGCTACGGATACCGCCGGATCACTGCCCTTCTGCGCGAGGCCGGTTGGGCGGTGAACGTGAAACGGGTCGAGCGCATCT
GGCGGCGGGAGGGGCTGAAGGTGCCACAAAAGCAACCAAAGAAGGGTCGGCTCTGGCTGAACGACGGGTCATGCATCCGTCTGCGGCCAGAGCGTTCGAA
CCATGTCTGGTCCTACGACTTCGTCGAAGCCCGGACCCACGATGGAAGGAAGTTCCGCATGCTCAATCTCATCGACGAGTTCAGCCGGGAGTGCCTGGCA
ATCCGGGTCGACCGGAGGCTCCGATCGACCGACGTCATCGACGTCTTGTCCGATCTCTTCATCCTGCGCGGTGTGCCGGATCATATACGGTCCGACAATG
GCCCGGAGTTCATCGCCAAGGCGGTGCGGGAATGGATCGTCGCCGTCGGCGCGAAGACCGCCTACATCGAGCCGGGGTCCCCCTGGGAGAACGGTTACTG
TGAGAGCTTCAATTCCAAGCTCCGCGACGAGCTGCTGAACGGGGAGATCTTCTACAGCCTCGCTGAGGCGAAGATTATCATCGAGAGCTGGCGCCGCCAT
TACAACACCAAGCGCCCGCACTCATCACTGGGGTATCGCCCGCCAGCTCCCGAGGCCATCCAGTGGCCGGCTTCGCCATCCGGAGCCGCTTCGCCGGCCA
CCCCAGTTGTAGCGCCAAGACCCGTAATGCACTAAGACTGAAACCGGACCACCCGATAGGGGCAGGCCA
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
279 bp92 aa67345+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MPQKKHKPEEIVAKLRQVDVLVSQGQSVAEAVRSISVTQFTYYRWRKEFGGLKTDQVKRLKELEKENERLRKAVSDLTLEKLILREAASGNF

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
942 bp313 aa2941235+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

PDAREAHPSGSGIGKLLSPARRRACIEHVRQKFRISERLACRVLGQHRSTQRKVPSGRADENVLTADIIALASQYGRYGYRRITALLREAGWAVNVKRVE
RIWRREGLKVPQKQPKKGRLWLNDGSCIRLRPERSNHVWSYDFVEARTHDGRKFRMLNLIDEFSRECLAIRVDRRLRSTDVIDVLSDLFILRGVPDHIRS
DNGPEFIAKAVREWIVAVGAKTAYIEPGSPWENGYCESFNSKLRDELLNGEIFYSLAEAKIIIESWRRHYNTKRPHSSLGYRPPAPEAIQWPASPSGAAS
PATPVVAPRPVMH

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
1169 bp389 aa671235+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MPQKKHKPEEIVAKLRQVDVLVSQGQSVAEAVRSISVTQFTYYRWRKEFGGLKTDQVKRLKELEKENERLRKAVSDLTLEKLILREAASGKLLSPARRRA
CIEHVRQKFRISERLACRVLGQHRSTQRKVPSGRADENVLTADIIALASQYGRYGYRRITALLREAGWAVNVKRVERIWRREGLKVPQKQPKKGRLWLND
GSCIRLRPERSNHVWSYDFVEARTHDGRKFRMLNLIDEFSRECLAIRVDRRLRSTDVIDVLSDLFILRGVPDHIRSDNGPEFIAKAVREWIVAVGAKTAY
IEPGSPWENGYCESFNSKLRDELLNGEIFYSLAEAKIIIESWRRHYNTKRPHSSLGYRPPAPEAIQWPASPSGAASPATPVVAPRPVMH

 

Blast result :
Comments
The third ORF is a putative ORFAB transposase reconstructed in silico by a possible -1 frameshift.
ISPmar2 (orfAB) is 85% aa similar to ISMdi16. ISPmar2 is 63% (ORF1) aa identical to ISMex5, 81% (ORF2) to ISNha4.
ISPmar2 has been identified by its transposition into entrapment vectors pMEC1 and pMMB2 (cI-tetA cassette). Upon transposition it generated 4 bp DRs or 15 bp deletion within the target site. As judged from DNA hybridization analysis ISPmar2 is present in 1 copy in the genome of P. marcusii DSM 11574.
References
1] Dziewit, L. and Bartosik, D. (2010) Direct submission
2] Dziewit, L., Baj, J., Szuplewska, M., Maj A., Tabin, M., Czyzkowska, A., Skrzypczyk, G., Adamczuk, M., Sitarek, T., Stawinski, P., Tudek, A., Wanasz, K., Wardal, E., Piechucka, E., Bartosik, D. (2012) PLoS ONE 7: e32277