The following sequence was obtained (written in 5\' to 3\' orientation) CACAAAGG
ID: 81117 • Letter: T
Question
The following sequence was obtained (written in 5' to 3' orientation)
CACAAAGGGC CATAAAAATG TTCATAATCT GGTGGGTGTG GTGGCTCATG CCTGTAATCC CAGCATTTG GGAGGCCAAG GTGGGAGGAT GCCTTGAGTC TAGGAGTTG AGAGATGCCT GGATAACACA GAGAGACCCT CATCTCTACA AAA
Question1) : Using a BlastN search, identify matches to the above sequence ( if the search results show sequences corresponding to a "human contig", these not an acceptable- choose sequences with a defined gene or sequence identity). Identify the name of the repetitive DNA sequence that is the best match. Remember that not all Blast hits are real, and you need to inspect the matches closely to identify real hits
Question 2:Using information you can find in journal articles (from NCBI for example) write a paragraph (no more than half a page) describing the biological features of the repetitive sequence you have identified. In your write up, include details such as a) in which species is the repeat found? b) estimation of copy number of the repeat in the genome c) the dispersion pattern of the repeat d) are there any associations of the repeat with disease?
Explanation / Answer
The best match for the above nucleotide sequence is given below; these nucleotides have the highest similarity,
Human Alu family interspersed repeat; clone BLUR1
Human DNA sequence from clone RP11-101O6 on chromosome
Macaca fascicularis complete genome, chromosome chr1
These are the close match for the given sequence.