Hello Dr. Perry, In addition to what Kayla recommends, you may want to read this paper which discusses some possible reasons why repeats are associated with inversions.
Principles of Genome Evolution in the Drosophila melanogaster Species Group Ranz JM, Maurin D, Chan YS, von Grotthuss M, Hillier LW, et al. PLoS Biology Vol. 5, No. 6, e152 doi:10.1371/journal.pbio.0050152 http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050152 On Thu, Dec 4, 2008 at 2:43 PM, Rodney Perry, Ph.D. <[EMAIL PROTECTED]> wrote: > I recently retrieved the DNA sequences at the 5' and 3' junctions where > an inversion occurs on 9q (#29497). This is a large inversion of almost > 2 Mb. I was looking at ~ 500 bp of sequence at each end and to my > surprise the sequences were 5' and 3' reads of the same sequence! I > don't know how far back past the 500 bp this goes back and I am confused > by this. Can you please explain this? > > > > The ~500 bp sequences at each end of the "inverted sequence" are below: > > > > (85,698,400) AAAATCAATATAC-5' Breakpoint- > > > TAAATATTCATCTAAAGATGTTAAAAAGATAGCAGGAGGTTACCCCAAAAGTAGAAGGAATTAAATAATAAA > GGGCAGAAATTAGTGAAATAGTGAACAAACTAATGAAATAATGAACAAACATACACTAGTGAGGATTAACAA > AGTCAAAAATTGTCTCTTTGAAGAGACTAATGAATTGGTAATTTTACTAGCTAGTGAAACTGCAAGAAAAAA > AAGTGAGAGAAGGCACAAATAATCAGGAATGAAAAAGGGGACATGTGACTACACAGTCCCCTTTATTCATTA > ATAAAGATATTAATGAATAAAAGACTATCATAAACAAACTTATGCCAATACATTTGAAAATTATATACAATG > GTCAAATTCCTAGAAAAATAAACCTTATCAAAACTGGAGGAAAAGAAAATACTAATATGATTTAATTCATAA > AACATACCCCCAAAGAAAATTTCCAGTCCCAAATGCTTAACAGGCTAATTCAACCA > (85,698,900)........ > > > > .......(87,639,800) > TCCCCCTATACCTGGAAAAGTGTGTGAAAATTGGTATTATTTCTTTCTTAAATGTTTGGTTGAATTAGCCTG > TTAAGCATTTGGGACTGGAAATTTTCTTTGGGGGTATGTTTTATGAATTAAATCATATTAGTATTTTATTTT > CCTCCAGTTTTGATAAGGTTTATTTTTCTAGGAATTTGACCATTGTATATAATTTTCAAATGTATTGGCATA > AGTTTGTTTATGATAGTCTTTTATTCATTAATATCTTTAGCTGTGTAGTCACATGTCCCCTTTTTCATTCCT > GATTATTTGTGCCTTCTCTCACTTTTTTTTCTTGCAGTTTCACTAGCTAGTAAAATTACCAATTCATTAGTC > TCTTCAAAGAGACAATTTTTGACTTTGTTAATCCTCACTAGTGTATGTTTGTTCATTATTTCATTAGTTCAC > TATTTCACCAATTTCTGCCCTTTATTATTTAATTCCTTCTACTTTTGGGGTAACCTCCTGCTATCTTTTTAA > CATCTTTAGATGAATATTTA (87,640,324) > > > > -3' Breakpoint-GTATATT (87,640,330) > > > > Thank you for your assistance. > > > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
