Bioinformatics
In case a gene name or a gene ID or an accession number for a sequence of interest is not available, the database of Ensembl is involved in providing an interface that allows the users to use the BLAST or the BLAT option to align the given sequence of interest to the genome. Before starting this, it has to be made sure that the species of interest is chose. In this case it will be Homo sapiens. On running the sequence, the default program which is set as BLASTN will provide the gene, against the genomic sequence.
On viewing the results, the BLAST shows a hit to chromosome full-length hit to chromosome
Next to view the hit, the The BLAST/BLAT track shows that where the given query sequence matches the genome, and allows the users to compare the hit to any known genes in the region.
Search process includes the following steps:
- Going to the Ensembl home page, BLAST/BLAT was selected. Then the given query sequence was entered. On running the sequence, it was seen that one hit is found.
Figure shows BLAST search for the genomic DNA
- Next the results were viewed which showed the following:
Figure shows results of the BLAST search.
Same is done for the promoter gene and the promoter sequence is found as below:
Figure shows BLAST search for protein sequence.
Figure shows results of the unknown mRNA.
The function of the protein of the mammary tissue is identified as:
Exon shuffling theory provides that the exon assumes a new function after it has been moved while exon retains its original function after it has been moved. However there is disagreement whether exon shuffling applies to both of these definition.
Here exon shuffling is proved to be right since even after the exon changes its position in the sequence, it has the same original functions as it had before. This is seen in the image below. This image shows similar phenotype for a different exon from the above one, however all the functions have remained the same (Ensembl.org 2018).
References
How to search Ensembl. (2018). Retrieved from https://www.ebi.ac.uk/training/online/course/ensembl-browsing-chordate-genomes/how-search-ensembl
Ensembl.org (2018). Retrieved from http://asia.ensembl.org/index.html
