Question

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Look up the RPL4 gene in Drosophila melanogaster (fruit fly) in Entrez Gene. (a) (2 marks)...

Look up the RPL4 gene in Drosophila melanogaster (fruit fly) in Entrez Gene.

(a) What is RefSeq accession number of the genomic sequence of the gene? What is the RefSeq accession number of the corresponding mRNA sequence of the gene?

(b) Identify the same gene in Bos taurus (cattle). What is the RefSeq accession number of the genomic DNA sequence of the RPL4 gene in this animal? What is the RefSeq accession number of the corresponding mRNA sequence?

(c) Using the Needleman-Wunsch algorithm, determine whether the two genomic se- quences of the gene in fly and cow are homologous. How do you know? Do the same with the corresponding mRNA sequences. Which of the two (genomic or mRNA sequence) Is more useful for drawing a conclusion regarding homology? Why does that type of sequence lead to a higher percent identity? To answer this question use the EMBOSS needle program with default parameters.

THIS IS THE ONLY INFORMATION GIVEN

Expert Solution

Enter the NCBI website and in the search bar, choose "Refseq" from the drop-down menu and then type "Drosophila melanogaster RPL4 "

A RefSeq database is a collection of curated and annotated sequences of DNA, RNA and protein.

a) Under results, click "refseq (4)" link on the left side, (4) indicates that there are 4 Refseq results. For the gene sequence, you would find "Drosophila melaongaster chromosome 3R" Find the accession number under the title as: Accession: NT_033777.3.

For the mRNA sequence, the result would be titled, "Drosophila melanogaster ribosomal protein L4 (RpL4), mRNA"

The Refseq accession number for the mRNA is

Accession: NM_079814.3

b) Repeat the search by keying in "Bos taurus RpL4"

The RefSeq gene accession number can be found in the results under RefSeq(8), meaning there are 8 results. The accession number for the gene sequence appears second in the list of results:

Accession: NC_037337.1

The RefSeq mRNA accession number would be:

Accession: NM_001014894.1, which appears first in the list of results.

c) In order to determine the homology between the two sequences from Drosophila melanogaster and Bos taurus, both the mRNA and the gene sequences can be copied/downloaded and saved in a word/notepad file. Then, they can be pasted in the EMBOSS -NEEDLE program available online.

The gene sequence of Drosophila melanogaster RPL4 can be obtained by clicking on the gene result and moving the cursor to the graphics window under "Genomic regions, transcripts and products" when you move the cursor to RPL4 within the window, it would show the gene details. Click the link under "FASTA view". A new tab would open with the gene sequence of 2068 nucleoties. Copy and paste the sequence in notepad/word document. Repeat the same for Bos taurus. The gene size for this species is 4,652 nucleotides.

The mRNA sequences for both the species can directly be obtained by clicking the "FASTA" link under the mRNA RefSeq result.

To check the homology between the RPL4 sequences of Drosophila melanogaster and Bos taurus, Open the EMBOSS-NEEDLE page and choose "DNA" from the drop-down menu. There are two slots to paste sequences. Paste the gene or mRNA sequence of the first species in the first slot and the second species in the second slot and hit "submit", wait for the results.

In the case of gene sequence alignment, the percentage similarity /identity between the two species is ~26%

In the case of mRNA sequence alignment, the percentage similarity/identity is ~57%

The mRNA sequence alignment would show a higher percentage similarity compared to that of the gene sequence as it is devoid of introns; the coding sequence is more specific and would match better. mRNA sequence is more useful in determining homology between sequences of different species for the same reason. The homology may be higher if the species are more closely related.

gladiator answered 8 months ago

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