Question

We have four tubes containing individual primers that are designed to amplify two particular regions of the human genome.

While organizing tubes, we accidently erased all the information regarding these tubes. Use the following web tools to figure

out which primer is paired with which another to amplify which region of human genome.

(UCSC In-Silico PCR: http://genome.ucsc.edu/cgi-bin/hgPcr?hgsid=568061131_Us1GaoCaBcZKgNTGBAA8MZeDDOz3)

Primer 1: 5’-GTTTGGAGACAACGCTGGCC-3’

Primer 2: 5’-CTGCCCAGGGCCTCACCACCA-3’

Primer 3: 5’-ACATTTGCTTCTGACACAAC-3’

Primer 4: 5’-AATTGGAAGCAAATGACATC-3’

Once you find out the genomic regions, explain what size of each PCR product you will obtain if you actually do PCR?

Also, describe what kind regions of these two PCR products are coming from (such as intron or exon).

Answer 1

First pair of primers are

Primer 1 (F): 5’-GTTTGGAGACAACGCTGGCC-3

Primer 4 (R): 5’-AATTGGAAGCAAATGACATC-3’

GTTTGGAGACAACGCTGGCCttttccagaggcgacctctgcatggtctctcgggcgctggggtccctgctagggccgtctgggctcaagctcctaatgccaaagacctactactctgggtgcctgccgctcaaccctttttctctgacctgctgtGATGTCATTTGCTTCCAATT

Product length: 175 bp

It is amplifying intronic region (chr7:117,479,963 - 117,480,137)

Second pair of primer are

Primer 2: 5’-CTGCCCAGGGCCTCACCACCA-3’

Primer 3: 5’-ACATTTGCTTCTGACACAAC-3’

CTGCCCAGGGCCTCACCACCAacttcatccacgttcaccttgccccacagggcagtaacggcagacttctcctcaggagtcagatgcaccatggtgtctgtttgaggttgctagtgaacacaGTTGTGTCAGAAGCAAATGT

Product length: 142 bp

It covers small portion of Exon 1, 1^st intron and small portion of Exon 2 (chr11: 5,226,930 - 5,227,071)

Note: please ignore below mentioned figure, by mistake ans for other question was added simultaneously.