PLEASE HELP ME. I HAVE HAVING SUCH A HARD TIME WITH THIS LAB!! -MOLECULAR BIOLOG

Question

PLEASE HELP ME. I HAVE HAVING SUCH A HARD TIME WITH THIS LAB!! -MOLECULAR BIOLOGY

In my spare time I have been cloning genes from the Mockingjay. The DNA sequence belows was isolated from a Mockingjay cDNA library

atgaacccccaagcggagctactctttgtcattagcctacttctaggaacaactatcaca atctcaagcaatcactgggttatagcctggaccggtcttgaaatcaatacactggctatc ctacccctaatcgcaaaatctcatcacccccgagctattgaagcagcgaccaaatacttc ctagtacaagcagccggctcaactctagtgctattctctagcataaccaatgcgtggtcc actggacaatgggatatcactcagctaacccacccaacatcttccctaattctaaccgca gccatttcgataaaactaggccttgcagcattccactttcgattcccagaagttttacaa ggctctcctgaaaccacgggtctccttctgtcgacagccataaaattcccgcccatcacc ctactatttatgacttctcagtcactcaaccccacactactaaccaccatggccattctt tccgtagccctgggaggatgaatgggtctaaaccaaacacaaacccgaaaaagtatggcc ttcacctctatctctcatccaggttgaatagcaatcattctagtatactgccctaaactt accctacttaacttttacatgtacagtgtgataactgctgccgtattcctaactctaaac tcaacaaaaactctaaaactatcaacactaataaccgcatgaacaagagcacctccactc aacactattctcctactaacacttctatctctagccggcctccctcccctaactggcttc ctgccaagatgactcatcattcaagaactaactaaacaggacatagccccagcagcaata atcatttcactcctgtcactactaggactcttcttcgaccttcgtcttgcatactgcgca acaatcacacttccaacacccactacaaaccacataaaacagtgacacgtcaacaaacca attaatgcctcaatcgccgttctaactacactctctatcatgctcctcccatattccccc atactatccaacattatataa

1) Would you predict there are any Mockingjay sequences in Genbank?

2) Use an appropriate DNA sequence analysis tool to determine what this gene encodes. Comment on the rational and be sure to include which organism is this gene most homologous to the one above derived.

3) what is the likely function of this gene and where is in encoded?

4) Use appropriate DNA sequence analysis tool online to determine with is the correct reading frame.

THIS IS THE LINK TO THE ANALYSIS TOOL FOR DNA SEQUENCES. http://blast.ncbi.nlm.nih.gov/Blast.cgi

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Is this the gene I should be looking at?? I found this on the BLAST and it has an E value of 0.0. Meaning most homologous to the gene I am testing?

Perisoreus canadensis isolate MVZ_182097_WA_Whatco NADH dehydrogenase subunit 2 (ND2) gene, complete cds; mitochondrial

Explanation / Answer

ANSWERS:

1) It is easy to predict that there will not be any Mockingjay sequences in GenBank as it has sequences of real animals and not fictional characters.

2) An appropriate DNA sequence analysis tool would be BLAST to find out which can be used to find out any sequence that is available within NCBI and also what this gene would encode, unless a nucleotide sequence for the query that you are looking for is already given. The homologous animal for this gene is Perisoreus canadensis i.e Grey Jay.

3) The gene that is coded is a type of NADH Dehydrogenase enzyme that is found in the mitochondria. NADH Dehydrogenases are flavo proteins that contain iron and sulfur centres in the core of the enzyme.

4) The E value is a statistical parameter in BLAST that determines the significance of the aligned sequences. The lesser the E value means lower is the chances of a random alignment between the two sequences;i.e there is a lower chance that the sequences will not be aligned or a higher chance that the sequences are homologous.

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