ISEc1

  • Family ISAs1
  • Group
MGE type ISRelated element(s) :
Isoform Synonym(s) H-rptB, RhsB, H-rptC1, RhsC, H-rptC2, H-
Accession numberTranspositionOriginHost
L02370 ND Escherichia coli
Escherichia coli ECOR-50
Escherichia coli K-12
DNA section
IS Length : 1291 bp

Ends


IR Length : 14/18

IRL : CAGGGAAAGATCATCAAAAGTTCACTTTTTGCACTAAATAATTCGCATTT
IRR : CAGGGCAAGATTACGAAAGCCCGCTCCCCGCAAGGACTGACGCCAGATAG

Insertion site


Left flankDirect repeatRight flankDR Length

DNA sequence

CAGGGAAAGATCATCAAAAGTTCACTTTTTGCACTAAATAATTCGCATTTTATGTTTAAAAATTGAGATATTCCTTATTACCTGAAGCTGTTTTTTATTG
CTTATACATGATCAAATACTCCTTACCTAATTAAGGAGAACAAAATGGAACTTAAAAAATTGATGGAACATATTTCTATTATCCCCGATTACAGACAAAC
CTGGAAAGTGGAACATAAATTATCGGATATTCTACTGTTGACTATTTGTGCCGTTATTTCTGGTGCAGAAGGTTGGGAAGATATAGAGGATTTTGGGGAA
ACACATCTCGATTTTTTGAAGCAATATGGTGATTTTGAAAATGGTATTCCTGTTCACGATACCATTGCCAGAGTTGTATCCTGTATCAGTCCTGCAAAAT
TTCACGAGTGCTTTATTAACTGGATGCGTGACTGCCATTCTTCAGATGATAAAGACGTCATTGCAATTGATGGAAAAACGCTCCGGCACTCTTATGACAA
GAGTCGCCGCAGGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATGAGAAATCTAATGAGATT
ACAGCTATCCCAGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCACAACTGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAA
AACAGGGAGGTGATTATTTATTCGCGGTAAAAGGAACCCAGGGGCGGCTAAATAAAGCCTTTGAGGAAAAATTTCCGCTGAAAGAATTAAATAATCCAGA
GCATGACAGTTACGCAATCAGTGAAAAGAGTCACGGCAGAGAAGAAATCCGTCTTCATATTGTTTGCGATGTCCCTGATGAACTTATTGATTTCACGTTT
GAATGGAAAGGGCTGAAGAAATTATGCGTGGCAGTCTCCTTTCGGTCCATAATAGCAGAACAAAAGAAAGAGCCAGAAATGACGGTCAGATATTATATCA
GTTCTGCTGATTTAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGA
AGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCA
GGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAATCTTGCCCTG
Protein section
ORF number : 1

 

ORF 1
LengthBeginEndStrandFusion ORF
1137 bp378 aa1451281+No
ORF function : Transposase
Chemistry : Unknow

ORF sequence :

MELKKLMEHISIIPDYRQTWKVEHKLSDILLLTICAVISGAEGWEDIEDFGETHLDFLKQYGDFENGIPVHDTIARVVSCISPAKFHECFINWMRDCHSS
DDKDVIAIDGKTLRHSYDKSRRRGAIHVISAFSTMHSLVIGQIKTDEKSNEITAIPELLNMLDIKGKIITTDAMGCQKDIAEKIQKQGGDYLFAVKGTQG
RLNKAFEEKFPLKELNNPEHDSYAISEKSHGREEIRLHIVCDVPDELIDFTFEWKGLKKLCVAVSFRSIIAEQKKEPEMTVRYYISSADLTAEKFATAIR
NHWHVENKLHWRLDVVMNEDDCKIRRGNAAELFSGIRHIAINILTNDKVFKAGLRRKMRKAAMDRNYLASVLAGSGLS

 

Blast result :
Comments
Escherichia coli K-12 contains 5 large repetitions (from 3.7 to 9.6 kb), representing nearly 1 % of the chromosome. These Rhs (Rearrangement hot spots) elements (RhsA to RhsE, scattered around the chromosome) provide homology for RecA-dependent rearrangements. These elements are present many but not all wild-type isolates of E. coli. The most prominent Rhs component is a giant core ORF whose features are suggestive of a cell wall surface ligand-binding protein. Each Rhs elements also contains another repeated sequence, the H-rpt element (Hinc-repeat) displaying features of typical Insertion Sequences, although no transposition activity has been detected yet. For the sake of clarity, the H-rpt DNA sequences B (RhsB), C1to C3 (RhsC), E (RhsE), and min.5 (Zhao et al., 1993) as well as H-rptF (Zhao and Hill, 1995) have been renamed ISEc1 to ISEc7, respectively.

October 1 2012 : the files ISEc2, ISEc3, ISEc4, ISEC6 and ISEc7 were deleted, there are isoforms of ISEc1. All the informations were added in this file.
Previous comments of ISEc2 (L02373):
ISEc2 is adjacent to ISEc3. It is a deleted variant that contains the first 380 bp of a normal element (Zhao et al., 1993). Its DNA is 94 % identical to that of ISEc3.
Previous comments of ISEc3 (L02373):
ISEc3 is located downstream of ISEc2. ISEc3 putative transposase is 98 % identical to that of ISEc1. ISEc3 378-aa ORF (144-1280) is however (probably) inactive due to the presence of a stop codon at position 17 (Zhao et al., 1993).
Previous comments of ISEc4 (L02373):
ISEc4 is located downstream of ISEc3. ISEc4 is a deleted variant that is missing the first 24 bp and a 313-bp fragment, about 65 bp from the 5' end (Zhao et al., 1993). Its DNA is 96 % identical to that of ISEc3.
Previous comments of ISEc6 (D83536):
ISEc6 is located 2 kb downstream of an Asp-tRNA. ISEc6 DNA sequence is 95 % identical to that of ISEc1. It corresponds to the last 290 bp of a entire element.
Previous comments of ISEc7 (U15125, U15126):
ISEc7 is present in Escherichia coli ECOR-50, but not in K-12 strains. The first 213 and the last 63 bp of ISEc7 have been determined so far (Zhao and Hill, 1995). Their identity to ISEc1 is above 93 %.The two Accession numbers correspond to right and left ends, complete sequence is unknow.
References
1] Sadosky, A.B., Davidson, A., Lin, R.J., and Hill C.W. (1989) J. Bacteriol. 171, 636-642.
2] Zhao, S., Sandt, C.H., Feulner, G., Vlazny, D.A., Gray, J.A., and Hill, C.W. (1993) J. Bacteriol. 175, 2799-2808.
3] Hill C.W., Sandt, C.H., and Vlazny, D.A. (1994) Mol. Microbiol. 12, 865-871.
4] Zhao, S., and Hill, C.W. (1995) J. Bacteriol. 177, 1393-1398.