ISCaa3

  • Family IS5
  • Group ISL2
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
NC_010830 ND Candidatus Amoebophilus
Candidatus Amoebophilus asiaticus 5a2
DNA section
IS Length : 911 bp

Ends


IR Length : 17/20

IRL : AGAGATCTTCTGAAACCTAAGGAATAAGCATAAATGTATAAATTAGGGAT
IRR : AGAGTTCTTCCGAAACTTAACATAAAAGTTCATAGTTATAAATTCCAGCA

Insertion site


Left flankDirect repeatRight flankDR Length
TTTACAATTCATTGAGCATATTA3
TATAGTTAGTATTGTATAAACAG3
AAAAATTTCCATTGGAGTATTTT3
TGTCCAAGCAATTTAAAAAATTA3
TAAAATCTATAGTATTCTTACAA3
GCCAACATATATTCTAGAAGGTA3
TTTGTATTTGATTGTAACAACCC3
GGAAATAGACAATTGCTCAGATA3
TATCGGCATTAATATTTTTA0
ATTGTTCAATATTATTATTT0
TTATAATATTAATGCCACAT0

DNA sequence

AGAGATCTTCTGAAACCTAAGGAATAAGCATAAATGTATAAATTAGGGATAAAAAAACAGAAAGATTAATGGAAAACAGTCATCTAAAAACCTTAAAGCC
AGAAGAATTCCGTCGCTTAACAGGCGTAAAGGCTGAGACCTTTGCCAAAATGTTAGCTATCATACAGAAAGCCATTCAAACAAAGAAAGCTAAAGTAGGG
CGGCCTAATAAACTGAGTTGTGAACAAATGTTTTTAATGACTTTAGAATATTTAAGAGAATACCGCACATACTTCCATATTTCAAAAAGTTATGGAATAA
GTGAGAGTAATTGCTATTATACCATCCGTTTTATTGAAGAGGCGTTAATTAAAAGTGGTCAATTCACTTTACCAGGCCGTAAAGCATTGTTAAAAAGCGA
TATGGAATATGCAGTAATCTTAATAGATGCTACAGAGAGCCCCATTGAGCGGCCTAAAAAAAGCAGCGATATTACTACTCAGGTAAAAAGAAACGACATA
CACTAAAGACGCAACTGGTTGTCGATAAGCAAACGCGAGCCATAATATGTAGTAGTTTTTCAAATGGAAAGCGGCATGACTTTCGCTTGTTTAAGGAATC
TAAGGTACATATAAGCCAGCATAGTCAAGCCATAGTAGATACAGGCTATCAAGGGTTAAAGAGGCTACATGACAAATCGCTTATGCCTAAAAAACGCAGT
AAAAAGCATTCTTTGACCAAAGCCGATAAGAGGAGTAATCAGCAATTAGCCAGCCAAAGGGTGCTTAGCGAGCATATAATTGGTATGCTCAAGCGGTTTA
AAATTTTAGCGGAGCGTTACAGAAATAGGAGAAAAAGATTTGGGCTACGCTTTAATCTTATTGCTGGAATTTATAACTATGAACTTTTATGTTAAGTTTC
GGAAGAACTCT
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
438 bp145 aa69506+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MENSHLKTLKPEEFRRLTGVKAETFAKMLAIIQKAIQTKKAKVGRPNKLSCEQMFLMTLEYLREYRTYFHISKSYGISESNCYYTIRFIEEALIKSGQFT
LPGRKALLKSDMEYAVILIDATESPIERPKKSSDITTQVKRNDIH

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
438 bp145 aa458895+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

KKQRYYYSGKKKRHTLKTQLVVDKQTRAIICSSFSNGKRHDFRLFKESKVHISQHSQAIVDTGYQGLKRLHDKSLMPKKRSKKHSLTKADKRSNQQLASQ
RVLSEHIIGMLKRFKILAERYRNRRKRFGLRFNLIAGIYNYELLC

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
827 bp275 aa69895+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MENSHLKTLKPEEFRRLTGVKAETFAKMLAIIQKAIQTKKAKVGRPNKLSCEQMFLMTLEYLREYRTYFHISKSYGISESNCYYTIRFIEEALIKSGQFT
LPGRKALLKSDMEYAVILIDATESPIERPKKKQRYYYSGKKKRHTLKTQLVVDKQTRAIICSSFSNGKRHDFRLFKESKVHISQHSQAIVDTGYQGLKRL
HDKSLMPKKRSKKHSLTKADKRSNQQLASQRVLSEHIIGMLKRFKILAERYRNRRKRFGLRFNLIAGIYNYELLC

 

Blast result :
Comments
ISCaa3 is 81% aa similar to ISCaa2.
The third ORF is a putative ORFAB transposase reconstructed in silico by a possible -1 frameshift.
References
1] ISfinder annotation (2010).

2] Lucas,S., Copeland,A., Lapidus,A., Glavina del Rio,T., Dalin,E., Tice,H., Pitluck,S., Chain,P., Malfatti,S., Shin,M., Vergez,L., Lang,D., Schmutz,J., Larimer,F., Land,M., Hauser,L., Kyrpides,N., Ovchinnikova,G., Horn,M. and Richardson,P. (2008) Direct submission Genbank.