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COURSE OF BIOINFORMATICS
2013-2014
Exam_30/01/2014
A
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Human ACOX3 gene
Slide 1
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1.
Report the Gene_ID, the chromosomal and genomic (in bp)
localization of the human ACOX3 gene
2.
How many different transcript isoforms exist for the ACOX3 gene?
Do they differ in their ending point (i.e.: last exon)?
3.
Is the ACOX3 gene involved in the etiology of any disorders? If yes,
annotate disorder name and corresponding MIM number
1.
Which are the genes contained in the genomic region spanning 50
kb upstream and 50 kb downstream to the ACOX3 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 identify a CpG island
putatively involved in the transcriptional regulation of the ACOX3 gene?
Describe some of the main features of the CpG island identified.
6.
In your opinion, does the identified CpG island physically overlap with
any other genomic DNA feature suggestive of transcriptional regulation?
7.
Report the Accession code of the reviewed ACOX3 protein. Which
protein domains, if any, are reported and where are they localized?
8.
Could you find a murine homologue of the human ACOX3 gene? Annotate
its GeneID and its genomic location.
Slide 3
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9. Do a multiple sequence alignment with the following amino acid
sequences (suggestion: use ClustalW2). In your opinion, which is
the region showing the higher level of identity?
>ACOX3_seq1
MASTVEGGDTALLPEFPRGPLDAYRARASFSWKELALFTEGEGMLRFKKTIFSALENDPLFARSP
>ACOX3_seq2
MGSLPEEKDSALWSDTPKGPLSAYRARASFNSGELLLFWDGQDVIHFKKTIFSTLENDPLFARSY
>ACOX3_seq3
MDEGIPDFPNGPLDIYRKKASFSWKDMMRFLEGDELIAFKQHVFRTLESDPLFARQPGEDVPVEQ
10. Retrieve the Accession numbers of the complete sequences from
which each of the above fragments was extracted and the species
they belong to.
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
ACOX3 gene? Recontruct the ontology of the GO terms in each of
the three categories in which the ACOX3 gene is annotated.
Slide 5
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12. In the ACOX3 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.