Here is a protion of the18S rRNA gene sequence from C. elegans… >gi|30525807|gb|

Question

Here is a protion of the18S rRNA gene sequence from C. elegans… >gi|30525807|gb|AY268117.1| Caenorhabditis elegans 18S ribosomal RNA gene, partial sequence

GCTTGTCTCAAAGATTAAGCCATGCATGCTTTGATTCATCAATGAAATTGCGTACGGCTCATTAGAGCAG ATATCACCTTATCCGGGATCCTCATATGGATAACTGCGGAAATACTGGAGCTAATACATGCAACTATACC CCAACGCAAGGCGGGGTGCAATTATTAGAACAGACCAAACGTTTTCGGACGTTGTTTGTTGACTCTGAAT AAAGCAGTTTACTGTCAGTTTCGACTGACTCTATCCGGAAAGGGTGTCTGCCCTTTCAACTAGATGGTAG TTTATTGGACTACCATGGTTGTTACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGA AACGGCTACCACGTCCAAGGAAGGCAGCAGGCGCGAAACTTATCCACTGTTGAGTATGAGATAGTGACTA AAAATATAAAGACTCATCCTTTTGGATGAGTTATTTCAATGAGTTGAATACAAATGATTCTTCGAGTAGC AAGGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCTCCTAGTGTATCTCGTTATTGCTG CGGTTAAAAAGCTCGTAGTTGGATCTAGGTTACGTGCCTCAGATTCGCAATTTGCGTCAACTGGGGGTCG TGACTTCTAATTTGCCGGTCTTGAGTCCTTAACAGGATTCTTAACAGGCATTGCAAGTTTACTTTGAACA AACCAGAGTGCTTCAAACAGGCGTTTTCGCTTGAATGGTCGTGCATGGAATAATAGAAAACGATTTCGGT TCAGTTTTATTGGTTTTACGGACTGAGATAATGGTTAACAGAGACAAACGGGGGCATTTGTATGGCCCCG TGAGAGGTGAAATTCTTGGACCGTGGCCAGACAAACTACAGCGAAAGCATTTGCCAAGAATGTCTTCATT AATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCCTAGTTCTGACCGTAAACGATGCCA TCTCGCGATTCGGAGGGTTTTTGCCCTGCCGAGGAGCTATCCGGAAACGAAAGTCTTTCGGTTCCGGGGG TAGTATGGTTGCAAAGCTGAAACTAAAGGAAATTGACGGAAGGGCACCACAAGGCGTGGAGCTTGCGGCT TAATTTGACTCAACACGGGAAAACTCACCCGGTCCGGACACCATTAGGACTGACAGATTGAAAGCTCTTT CTCGATTTGGTGGTTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCTGGTTTATTCCGATA ACGAGCGAGACTCTAGCCTGCTAAATAGTTGGCGAATCTTCGGGTTCGTATAACTTCTTAGAGGGATAAG CGGTGTTTAGCCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCG TGCTACACTGGTGGAGTCAGCGGGTTTTTCCTATGCCGAAAGGTATCGGTAAACCGTTGAAATTCTTCCA TGTCCGGGATAGGGTATTGTAATTATTGCCCTTAAACGAGGAATGCCTAGTAAGTGTGAGTCATCAGCTC ACGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTATCCGGGACTGAACTGATTCGAGAAGA

1. Given the sequence above, choose forward and reverse primers that will amplify the entire BOLDED portion of the 18S rRNA gene.

a. Underline the places on the sequence where your primers will bind. Then type the sequences of your primers below and indicate the 5’ and 3’ ends. Remember that the 3’ or reverse primer is the reverse complement of the template (think about which direction DNA extends). Always write out sequences in the 5’ to 3’ orientation.

i. Forward primer = Type answer here

ii. Reverse primer = Type answer here

Explanation / Answer

(i) Forward primer : TGGATAAGTTTCGCGCCTGCTGC

(ii) Reverse primer : GAAATTCTTGGACCGTGGCCAGA

Underlining the places on the sequence where the primers will bind

GCTTGTCTCAAAGATTAAGCCATGCATGCTTTGATTCATCAATGAAATTGCGTACGGCTCAT
TAGAGCAGATATCACCTTATCCGGGATCCTCATATGGATAACTGCGGAAATACTGGAGCTAA
TACATGCAACTATACCCCAACGCAAGGCGGGGTGCAATTATTAGAACAGACCAAACGTTTTC
GGACGTTGTTTGTTGACTCTGAATAAAGCAGTTTACTGTCAGTTTCGACTGACTCTATCCGG
AAAGGGTGTCTGCCCTTTCAACTAGATGGTAGTTTATTGGACTACCATGGTTGTTACGGGTA
ACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCACGTCCAAGGAA

GGCAGCAGGCGCGAAACTTATCC

ACTGTTGAGTATGAGATAGTGACTAAAAATATAAAGACTCATCCTTTTGGATGAGTTATTTC
AATGAGTTGAATACAAATGATTCTTCGAGTAGCAAGGAGAGGGCAAGTCTGGTGCCAGCAGC
CGCGGTAATTCCAGCTCTCCTAGTGTATCTCGTTATTGCTGCGGTTAAAAAGCTCGTAGTTG
GATCTAGGTTACGTGCCTCAGATTCGCAATTTGCGTCAACTGGGGGTCGTGACTTCTAATTT
GCCGGTCTTGAGTCCTTAACAGGATTCTTAACAGGCATTGCAAGTTTACTTTGAACAAACCA
GAGTGCTTCAAACAGGCGTTTTCGCTTGAATGGTCGTGCATGGAATAATAGAAAACGATTTC
GGTTCAGTTTTATTGGTTTTACGGACTGAGATAATGGTTAACAGAGACAAACGGGGGCATTT
GTATGGCCCCGTGAGAGGTG

AAATTCTTGGACCGTGGCCAGAC

AAACTACAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTT
CGAAGGCGATTAGATACCGCCCTAGTTCTGACCGTAAACGATGCCATCTCGCGATTCGGAGG
GTTTTTGCCCTGCCGAGGAGCTATCCGGAAACGAAAGTCTTTCGGTTCCGGGGGTAGTATGG
TTGCAAAGCTGAAACTAAAGGAAATTGACGGAAGGGCACCACAAGGCGTGGAGCTTGCGGCT
TAATTTGACTCAACACGGGAAAACTCACCCGGTCCGGACACCATTAGGACTGACAGATTGAA
AGCTCTTTCTCGATTTGGTGGTTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGT
CTGGTTTATTCCGATAACGAGCGAGACTCTAGCCTGCTAAATAGTTGGCGAATCTTCGGGTT
CGTATAACTTCTTAGAGGGATAAGCGGTGTTTAGCCGCACGAGATTGAGCGATAACAGGTCT
GTGATGCCCTTAGATGTCCGGGGCTGCACGCGTGCTACACTGGTGGAGTCAGCGGGTTTTTC
CTATGCCGAAAGGTATCGGTAAACCGTTGAAATTCTTCCATGTCCGGGATAGGGTATTGTAA
TTATTGCCCTTAAACGAGGAATGCCTAGTAAGTGTGAGTCATCAGCTCACGTTGATTACGTC
CCTGCCCTTTGTACACACCGCCCGTCGCTATCCGGGACTGAACTGATTCGAGAAGA

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