It is known gene H in chickens is responsible for fatty acid metabolism. You won

Question

It is known gene H in chickens is responsible for fatty acid metabolism. You wondered if bovines possess a homologous gene even though we know that the chicken is a non-mammal and non-rumen animal. You are asked to design an experiment to prove or disprove the idea that the bovine genome contains a gene H homolog. Make sure to include the platform you are going to use, why you chose that particular system, and a brief description of the experimental design (times, control, sample collections, etc.), analysis, and data interpretation.

Explanation / Answer

To find out the homologue of the gene H between chicken and bovine the easiest and the quickest way is bioinformatics. In these days most of the genome from known organism has been analysed and the information has been stores in several data bases for future use.   

For chicken H gene, go to NCBI website. This contains a huge database for genome, proteome, etc.

First find the homologue gene name and the name of the organism (If possible use the scientific name). Search in the homologue database with this information.

Your search leads to finds multiple records, click on the specific H-gene name along with the species. The name of the homologues gene is found in the list. If the similar homologues are present in the bovine it will appear in the list.

If there are no result found check the gene data base of NCBI with similar approach. Click on the desired record and then click on the homologue gene like appeared on the right side of the page.

If no homologue gene found this way then find out the protein name and its accession number (For example: NP_049403) from the data base. Then go to the Protein data base with this accession number. Search for it. On the right side of the report you will find ‘more about abc gene’ click it and search the homologue gene from that result following the similar approach in the previous steps.

If there is no ‘more about abc gene’ appears the probably NCBI does not have any previous homologue of H gene in bovine in their database. Then goto the potential homologues by clicking the blue links on the top right of the page. This will provide you some name of protein which may the homologues of Gene-H.

Search the data base for the proteins with accession number provided. Then find out the Nucleotide data base for the nucleotide sequence of respective proteins with the help of

Nucleotide Accession Number (like NM_048274). Go to the FASTA format of that sequence. Collect the FASTA FORMAT of the nucleotide sequence of respective proteins and then go to BLAST Home Page.

There you and click "nucleotide blast" under Basic BLAST and paste the sequence in the query box.

The result will show the similarity between the homo genes from which you can understand they are homologue or not.

Another way is BLAST the data base with the Chicken H gene sequence with Bovine by selecting the Bovine in   "Organism" box.

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