TD Bioinformatique du 17/11/2020

1) Go to the region from 319370000 to 32633000 bp on human chromosome 13.

a) On which cytogenetic band is this region located?
Q13.1
b) How many contigs make up this portion of the assembly?
8
2) Zoom in in the BRCA2 gene.
a) Configure this page to turn on the Tilepath Track in this view. What is this track?
Vecteur d’amplifiction
b) Are there any Tilepath clones that contain the complete BRCA2 gene?
1

3) Find the human MYH9 (myosin, heavy chain 9, non-muscle) gene, and go to the Gene
tab.
a) On which chromosome and which strand of the genome is this gene located
22 q12.3
b) How many transcripts (splice variants) are there and how many are protein
coding
11 transcrits 3 codants
c) What is the longest transcript and how long is the protein it encodes?
7451 bp pour MYH9 201 protein = 1960aa
d) Which transcript is the best quality
201 psq il a une sequence consensus
e) Are there any diseases associated with this gene according to OMIM (Online
Mendelian Inheritance in Man)?
Yes 2
surdité et Macrothrombocytopenie and les inclusions de granulocytes avec ou
sans néphrite ou surdité de perception

4) The transcript MYH9-201

A) How many exons does it have?
41
B) Are any of the exons completely or partially untranslated?
2 exons
C) Is there any associated sequence in UniprotKB/Swiss-Prot?

A0A024R1N1 identifiant uniprot = P35579

D) What are some functions of MYH9 according to the Gene Ontology consortium?
Niveau moléculaire, elle lie l’actine et l’ATP au niveau cellulaire role dans
l’adhésion etablissement de la polarité des cellules T, dans la phagocytose…

5) Phenylketonuria is a genetic disorder caused by an inability to metabolise

phenylalanine in any body tissue. This results in an accumulation of phenylalanine,
 causing seizure and mental retardation. Search for phenylketonuria from the
Ensembl home page.
a) What gene is associated with this disorder?
PAH
b) How many protein-coding transcripts does this gene have?
6 parmis 18
c) What is the MIM disease identifier for this gene?
MIM : 612349

6) The SNP rs1738074 in the 5’ UTR of the human TAGAP gene has been identified as a
genetic risk factor for a few diseases.
a) In which TAGAP transcript is this SNP found?

b) What is the least frequent genotype for this SNP in the Yoruba (YRI) population?

c) What is the ancestral allele? Is it conserved in the eutherian mammals?

d) With which diseases is this SNP associated? Are there any known risk (or
associated) alleles?

7) Find the location tab for the APOE gene

a) Is there a regulatory feature annotated at the 5’ end of this gene?
b) What kind of feature is it and what is its stable ID?
c) In which cell types is this feature active?
d) Can you observe transcription factor binding in HEPG2 cells? Which transcription
factor(s) – name at least 10

Bonus exercise:
Microarray data suggests that differential SERPINB10 expression is involved in prostate
cancer. You have a medium sized, European, case-control population with 500 cases and 500
controls. You can only afford to genotype a couple of SNPs to see if any are associated with
prostate cancer risk in your cohort.
Which SNPs do you pick and why?