Question

I would just like to check my work on this.

Using bioinformatics.

1. a) Find Accession NG_016141.1. what is the name of this sequence and on what chromosome is it located?

b) The e-value represents the probability that the sequence you are testing does NOT match the sequence in the database. Let’s say you have a sequence from humans that did not have a known function. It matches to the GFP sequence from jellyfish with an e-value of 1e-2 and the CDK sequence of the yeast S. cerevisae with an e-value of 1e-8. Which of these two sequences is a closer match that would lead to further testing (don’t forget to tell us why you determined this)?

c) How and where specifically do the taster and nontaster alleles differ? What is the most common (predominant) form (variant) of each one for the taster and non-taster alleles?

d) What are the accession numbers for the non-taster and taster alleles?

e) What is the full length of the nontaster allele in nucleotides?

Answer 1

1. NG_016141.1 is the accession number for the nucleotide sequence of Homo sapiens taste 2 receptor member 38 (TAS2R38). It is located on Chromosome 7.

Homo sapiens taste 2 receptor member 38 (TAS2R38), RefSeqGene on chromosome 7 NCBI Reference Sequence: NG_016141.1 FASTA Graphics Go to: LOCUS NG_016141 8143 bp DNA linear PRI 31-MAY-2020 DEFINITION Homo sapiens taste 2 receptor member 38 (TAS2R38), RefseqGene on chromosome 7. ACCESSION NG_016141 VERSION NG_016141.1 KEYWORDS RefSeq; RefSeqGene. SOURCE Homo sapiens (human) ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo. COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from AC073647.9. This sequence is a reference standard in the RefSeqGene project.

Ans 2: E-value gives the probability of finding a matched sequence by chance. Lower the E-value, lower is the probability of a random match and more is the significance of the resultant hit and vice versa.

Acc. to the question, E-value for GFP sequence from jellyfish is 1e-2 is much greater than the E-value for the CDK sequence of the yeast S. cerevisae that is 1e-8. Hence, CDK sequence of the yeast S. cerevisae is a better/closer match for further testing.

Ans 3: The difference between the taster and non-taster alleles is due to the combination of 3 SNPs. The positions of the SNPs are:

• Position 145: Codon changes from CCA (Proline) in taster to GCA (Alanine) in non taster due to mis-sense mutation.
• Position 785: Codon changes from GCT(Alalnine) in taster to GTT (Valine) in non taster with no sequence alteration.
• Position 886: Codon changes from GTC (Valine) in taster to ATC (Isoleucine) in non taster. (Missense variant)

Ans 4: Accession number for non taster alleles: rs10246939, rs1726866, rs713598.

Ans 5: taster allele is of around 1142 bp and non-taster allele is of 303 bp long