Identifying And Characterizing The Gene And Promoter Sequence Using Ensembl

Two genomic sequences and one mRNA sequence is available for analysis. One gonomic sequence is the gene sequence and the other is the promoter sequence for the gene. You have cloned and sequenced this novel (never sequenced or identified before) gene and promoter from human mammary tissue.

You have also characterized the mRNA of the gene by identifying the exon/intron boundaries. The exons are located at base pairs 1-510, 1401-1640, 2299-2538, 2941-3081, and 3672-5121 of the genomic sequence. After some initial database searches, you think that the gene is derived by exon shuffling between several different genes.

Your job is to identify and characterize the promoter, gene, mRNA, and protein and decide if your exon shuffling theory is correct.

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.

The steps will be followed in a sequential manner:

1. Start at the Ensembl home page.
2. Click on BLAST/BLAT at the top of the page.
3. Enter the sequence at the top of the BLAST/BLAT view.
4. Make sure your species of interest is chosen (Homo sapiens).
5. Click RUN. The default program is BLASTN, against Genomic sequence ("How to search Ensembl", 2018)

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. 

1. 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.

2. Next the results were viewed which showed the following:

Same is done for the promoter gene and the promoter sequence is found as below:

The function of the protein is given as:

Exon shuffling theory provides that the exon that has been shuffled tends to assume a new function after it has been moved however according to this theory, the exon retains its original function even 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 https://asia.ensembl.org/index.html