IS120

  • Family IS3
  • Group IS150
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
NC_009012 Y Clostridium thermocellum
Clostridium thermocellum ATCC 27405
Clostridium thermocellum
DNA section
IS Length : 1447 bp

Ends


IR Length : 10/12

IRL : TATAATGATACCAAAAATTAAGACAGACAAAACAGCCCAAATAAGTTAGA
IRR : TATAATGCTCCCCATTGTCAAGACAGTTTTTTAGCTTTTCTAAGTTAGTT

Insertion site


Left flankDirect repeatRight flankDR Length
NNNGGCTTGGTTATGCCGGTACT3
CAAAAAGCGTATTGACATAAAGTATATGAAGACAAAA3
CAATACATTTGAAGAGATACCGTCAAATAAAGAGTAA3
TTTATTACCCAATTCAGGAACTTAAAGCATTTGACGAGTC0
TCTGCAGGACGGCCTCATACAACCTCTGGGCTGTAAT3
TAGGTGAATTTGCAGCTCTATGTACATTTATATTTGT3
ATCTGCGATTTTTGAATCTTTATCTGAACGTCAGGAT3
CTTATCAAAAAACGAACCCGTTTCTATATACATCTAT3
GTATATTGAGCTCTTTGCAGAGCCTGTACACCTTTTT3
CGCGGTTACCTTAGATTTATCTTCCTGATTGATTTTA3
AAAGTTTGTACACATAATAGTATATTAAAGGGACCT4
TTTCTATAAGAAAAAAGCATCGGCAGAATTTAATTCC3
TGTAGCATTAAGTGGTATTTCTCTATATTTCATACCT3
AGTCCACTCTTTCGGCTGTAACGATAATTGTTTTAAC3
GAATAGCAGTTATAGAAGGATATAATGGTCTTTAAGCCTA0
TGTCGTGGGAAATTTGAAATCATAGTATAATAATACT3
GCATCCACAATGAAGTGCTTCGTTGCAGGCACGCTGA3
AGCATGACGGTCAGGAAAATTGCACACCATTTTTTTA3
TCAATTACGGTCGGCTTTTCTGTCATTAAAAGATAAC3

DNA sequence

TATAATGATACCAAAAATTAAGACAGACAAAACAGCCCAAATAAGTTAGAATGGAACTATGGAAAAGAGAAAACATTTTACACCTGAACAAAAAGCAAAA
ATAGTGATTGAGGTCATCAAGGGAGAAAGAACGCTGAATGAGATTGCTGCAGAATATGGAATTCATCCAAACCTGTTAAGTCGCTGGAAGACTGAATTCA
TAAGCAATGCGGGCAGAGTATTCAGCAAGGAAACTGATGAAGTAGAGAAGGTCAAACAGTCGTATGAAAAGGAGAAGGACGAACTGCTTAAGCAAATTGG
TCAACTATCATATGAGGTTGCCTGGCTTAAAAAAAAATCTGGCCTCCTCTAAATCCCGAGAAGACCGCATGAAAATGATTGATAGAAATGAGAAGAAACT
CAGCATAACAAGGCAAGCAGAATTATTGAGCTTAAACCGTACGAGCGTTTACTACAAGCCTGCTCCGGTAAATGAGGAGGAATACCTGATTAAGCGTATC
ATTGATGAAATTTACGCGTCTTATCCGGAATATGGCTATCGCAGGATGACAAGTATATTGAACAAGGATTATCACATTCATATCAATCGAAAACGGACCC
GGCGTTATATGAGGGAAATGGGCATACATGGATTCTGTCCTGGCCCCAACCTCAGCAAACGAATACATGGTAAGAATTTGTATCCATATCTGTTGAGAAA
CTTGAAAATTGATCATCCTAATCAGGTATGGTCCATAGATGTGACCTATTGCCGAATGAAACGCGGTTTCATGTATATGGTTGCAATAATAGACTGGTAT
TCTCGGTATATTGTTGGGTTTGAACTATCAAACACTCTTGATAAGACATTCGTCATAGAAGCAATCCAAAAGGCCATAAAGCGATATGGCAAGCCTGAAA
TCATGAACAGTGATCAAGGCTCACAGTTTACCAGTGATGATTACATAAATCTATTAAAAAATAACGGTATCAAAATATCTATGGATGGAAAAGGAAGAGC
ATTAGACAACCAAAGGATAGAACGATTTTTCCGTTCCTACAAGTGGGAGAAACTTTATCTTGAAGAGTGCGAAACGGTACAACAACTTAGACAAATCACA
AAGGAATATGTGGAGCACTATAACCATAGGAGACCGCACCAGTCATTGGATTACAAAACACCGGCAGAGTATTACTTTGGAGGATATGACCAGCTACTGG
CAGTTGTATAGAATTATGGGGCTCCGCCCCAAACCCCGTCCTCACCGGAAGGCAGCCGGTCTGTCATAACAGACCGGAAAGCAAAAGGATATATGTCCAA
AGGATGTCAAGGGTCAAGATGAACTCGCTTACGCTCGCCCTTGACATCCTCCAACAGAGTGCACAGTTGTAAAGATTATACAAAATTAAGAAAGGAGAAC
TAACTTAGAAAAGCTAAAAAACTGTCTTGACAATGGGGAGCATTATA
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
294 bp97 aa59352+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MEKRKHFTPEQKAKIVIEVIKGERTLNEIAAEYGIHPNLLSRWKTEFISNAGRVFSKETDEVEKVKQSYEKEKDELLKQIGQLSYEVAWLKKKSGLL

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
966 bp321 aa2461211+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

RRSNSRMKRRRTNCLSKLVNYHMRLPGLKKNLASSKSREDRMKMIDRNEKKLSITRQAELLSLNRTSVYYKPAPVNEEEYLIKRIIDEIYASYPEYGYRR
MTSILNKDYHIHINRKRTRRYMREMGIHGFCPGPNLSKRIHGKNLYPYLLRNLKIDHPNQVWSIDVTYCRMKRGFMYMVAIIDWYSRYIVGFELSNTLDK
TFVIEAIQKAIKRYGKPEIMNSDQGSQFTSDDYINLLKNNGIKISMDGKGRALDNQRIERFFRSYKWEKLYLEECETVQQLRQITKEYVEHYNHRRPHQS
LDYKTPAEYYFGGYDQLLAVV

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
1153 bp384 aa591211+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MEKRKHFTPEQKAKIVIEVIKGERTLNEIAAEYGIHPNLLSRWKTEFISNAGRVFSKETDEVEKVKQSYEKEKDELLKQIGQLSYEVAWLKKKNLASSKS
REDRMKMIDRNEKKLSITRQAELLSLNRTSVYYKPAPVNEEEYLIKRIIDEIYASYPEYGYRRMTSILNKDYHIHINRKRTRRYMREMGIHGFCPGPNLS
KRIHGKNLYPYLLRNLKIDHPNQVWSIDVTYCRMKRGFMYMVAIIDWYSRYIVGFELSNTLDKTFVIEAIQKAIKRYGKPEIMNSDQGSQFTSDDYINLL
KNNGIKISMDGKGRALDNQRIERFFRSYKWEKLYLEECETVQQLRQITKEYVEHYNHRRPHQSLDYKTPAEYYFGGYDQLLAVV

 

Blast result :
Comments
Unlike the other IS3 family members, fusion between ORFA and ORFB of IS120 requires a +1 translational frameshifting. IS120 ORF2 is 30 % identical to that of IS150.
The third ORF is a putative ORFAB reconstructed in silico.
References
1] Snedecor, B., Chen, E., Gomez, R.F. (1983) in Proc. IVth Int. Symp. Genet. Industr. Microorg., 1982, pp. 356-360.
2] Chandler, M., and Fayet, O. (1993) Mol. Microbiol. 7, 497-503.