QuBi/modules/biol302

BIOL 302 Lab: Bioinformatics Exercises

[Link to BIOL302 page, if one exists]

Identification of mdm2 Splice Variants Using BLAST

Objectives

• Learn to use Genbank database and BLAST tool to analyze nucleotide sequences
• Use BLAST to identify

Exercise

Genbank Accession #	cDNA Clone	Description	Cell Line	Length (bp)
AF527840		Genomic DNA		34,088
EU076746	P2-MDM2-C1	cDNA missing exons 5-9 & 11	MANCA	427
EU076747	P2-MDM2-10	cDNA missing exon 10	ML-1	842
EU076748	P2-MDM2-C	cDNA missing exons 5-9	A876	505
EU076749	P2-MDM2-FL	Full-length cDNA	SJSA-1	845

Explore the annotation for AF527840.

The sequences on the genbank database have annotations associated with them. Some sequences are richly annotated to contain all of the details you would want, and other sequences may have almost no annotations at all. The sequence you are about to explore is well annotated with details such as exon locations and nucleotide variablility. Use the annotations to complete the following tasks and questions.

1) DRAW a diagram of this gene, including its introns/exons, 3'/5' UTRs, +1. (Note: this diagram is going to be very handy for the last set of questions.) - Label each feature with its coordinates. For example, if an exon starts at 500bp and ends at 1000bp, label it as such. - Label the diagram with basic information, such as the gene's name and th organism's species. - The drawing does not have to be exactly to scale, a reasonable effort should be made to do so. Put length markers on your drawing (for example, every 5000bp.) - The mRNA annotation states which segments are used to create mRNA, and the CDS annotation states which parts actully code amino acids (CDS = coding sequence).

2) How does the sequence vary at positions X, X, and X for this gene?

3) What kinds of repeat regions can be found in this gene?