Bio-Info week 3 assignment

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Rutgers University *

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Biology

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Jan 9, 2024

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Tools for Bioinformatic Analysis Week3- Ensembl Genome Browser (30 points) Exercise 1- Guided activity- To learn how to browse your way to a particular chromosome band and locate genes that way. i. How many protein encoding transcripts does this gene produce? Please give Transcript ID for each. (4 points) This gene produces 8 protein-encoding transcripts. They are: Transcript: ENST00000006777.11 Transcript: ENST00000318622.8 Transcript: ENST00000428119.1 Transcript: ENST00000468304.1 Transcript: ENST00000467406.2 Transcript: ENST00000466232.5 Transcript: ENST00000468644.5 Transcript: ENST00000476218.1 ii. LIST three nonsynonymous variants- two different missense (pick two different amino acids that are affected) and one nonsense (stop gained)/ frameshift in the table below: (9 points Variant ID Map Location aka Chromosome bp Alleles (Change at gene level) Amino acid # affected Change in amino acid Type rs1369947128 7: 75,879,087 C/A/G/T 2 A/E Missense rs1554541927 7: 75,879,046 G/T 5 G/V Missense rs782504216 7:75879115 G/A/T 11 W/C Stop gained

Exercise 2- Guided activity- In this exercise, we will navigate to the gene page directly without looking into chromosome regions. i. Find the mouse CLOCK gene. To which chromosome does it map- give complete location? Is it on the forward or reverse strand? (2 points) Chromosome 5: 76,357,715-76,452,639- Reverse Strand Exercise 3: Use e75 version of ensembl not the current. Type in your browser: e75.ensembl.org- this will take you to the archived 75 th version of ensembl. This is non guided activity- if you have forgotten the steps- you would need to watch the demos again. (a) Find the human MYH9 (myosin, heavy chain 9, non-muscle) gene, and go to the Gene tab . i. On which chromosome and which strand of the genome is this gene located? (1 point) Chromosome 22: 36,677,327-36,784,063-Reverse Strand ii. How many transcripts (splice variants) are there? (1 point) There are 11 transcripts in total. iii. How many of these transcripts are protein-coding? (1 point) 3 transcripts are protein-coding. iv. What is the longest transcript, and how long is the protein it encodes? (1 point) Transcript: MYH9-001 ENST00000216181; Length-1960 AA v. Which transcript has a CCDS record associated with it? (1 point) Transcript: MYH9-001 ENST00000216181 (b) Click on Phenotype at the left side of the page. vi. Are there any diseases associated with this gene, according to MIM ( Mendelian Inheritance in Man )? If so, name one. (1 point) Yes, there are diseases associated with this gene. One of them is EPSTEIN SYNDROME (c) In the transcript table, click on the transcript ID for MYH9-001, and go to the Transcript tab. vii. How many exons does it have? (1 point) 41 exons viii. Have a look at the Ontology table view for the transcript. What are some functions of MYH9- 001? (3 points) Some of the functions are- Microfilament motor activity, Act independent ATPase, Cell Motility, Cell adhesion, and Cell organization.

Exercise 4 – Exploring a genomic region in humans: Use the e75 version of Ensembl not the current. Type e75.ensembl.org in your browser. (a) Go to the region from bp 32,448,000 to 33,198,000 on human chromosome 13. i. On which cytogenetic band is this region located? (1 point) q13.1 ii. How many contigs make up this portion of the assembly. Name them. (contigs are contiguous stretches of DNA sequence that have been assembled solely based on direct sequencing information)? (2 points) There are 7 contigs in total to make up this portion of the assembly. AC002525.1 AL137143.8 AL1386692.26 AL445212.9 AL137247.14 Al353665.13 Z84467.1 (b) Zoom in on the BRCA2 gene. (First find and click on BRCA2 in this region- in pop up click on Location- this will Zoom it in BRCA2 region) iii. Are there any BAC clones that contain the complete BRCA2 gene? Name it. (1 point) (In order to look for BAC clones, you would need to add a track- from left pane select configure this page, in the pop up search for BAC clone- a track called TILEPATH will appear- add that track and save the page). Your webpage will get update- scroll all the way bottom to see if there is any gold color BAC clone for BRCA2. Yes, there are BAC clones that contain the complete BRCA2 gene. It is- RP11-37E23 (d) Add the track with RefSeq gene models. iv. Has RefSeq annotated the BRCA2 gene? If so, how many transcripts have been annotated? Do they differ from the Ensembl transcripts? (1 point) Yes, RefSeq has annotated the BRCA2 genes, A total of 5 transcripts have been annotated. They do not differ from the Ensemble transcripts.

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