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COURSE OF BIOINFORMATICS
2013-2014
Exam_31/01/2014
B
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Human ATP2B3 gene
Slide 1
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1.
Report the Gene_ID, the chromosomal and genomic (in bp)
localization of the human ATP2B3 gene
2.
How many different transcript isoforms exist for the ATP2B3
gene? Where are the differences among the different isoforms
located?
3.
Is the ATP2B3 gene involved in the etiology of any disorders? If
yes, annotate disorder name and corresponding MIM number
4.
Which are the genes contained in the genomic region spanning 50
kb upstream and 50 kb downstream to the ATP2B3 gene? Is there
any difference between RefSeq genes and UCSC genes?Annotate
the official Gene symbols and the Gene_IDs of RefSeq genes in the
region.
Slide 2
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5.
In the genomic region previously defined, could you find a SNP identified
through a GWAS study? Report the ID of the SNP and the disease to
which it was associated.
6.
In the same genomic region, is there any evidence of the presence of
other SNPs reported in the literature? In your opinion, is there any
evidence that the SNPs you have identified are correlated to the ATP2B3
gene?
5.
Report the Accession code of the reviewed ATP2B3 protein. Which
protein domains, if any, are reported and where are they localized?
6.
Could you find a murine homologue of the human ATP2B3 gene?
Annotate its GeneID and its genomic location.
Slide 3
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9. Do a comparison between the ATP2B3 protein sequences encoded
respectively by the human and the rat genes. Report the
percentage of identities and of positives. Do the same between the
human and the Neurospora crassa proteins.
9. Do a Multiple Sequence Alignment (suggestion: use ClustalW2)
with the human, rat and Neurospora protein sequences. In your
opinion, the N-terminal and the C-terminal portion of the three
proteins show the same level of homology? Please, make your
comment about the obtained alignment.
Slide 4
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11. Using the Gene Ontology database could you infer the cellular
component, the biological process and the molecular function of
ATP2B3 gene? Recontruct the ontology of the GO terms in each of
the three categories in which the ATP2B3 gene is annotated.
Slide 5
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12. In the ATP2B3 3’ UTR, can you recognize any miRNAs binding
sites predicted by at least two different algorithms? Annotate
names, binding site position and the accession codes for
some of the predicted miRNA.