1. COURSE OF BIOINFORMATICS 2013-2014 Exam_30/01/2014 A

2. Insert the requested information: Name and Surname: Matricula Number: E-mail address: (I will contact you at this address!!)

3. Human ACOX3 gene

4. Slide 1 remember to annotate the source of the information 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.

5. Slide 2 remember to annotate the source of the information 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.

6. Slide 3 remember to annotate the source of the information 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? 10.Retrieve the Accession numbers of the complete sequences from which each of the above fragments was extracted and the species they belong to. >ACOX3_seq1 MASTVEGGDTALLPEFPRGPLDAYRARASFSWKELALFTEGEGMLRFKKTIFSALENDPLFARSP >ACOX3_seq2 MGSLPEEKDSALWSDTPKGPLSAYRARASFNSGELLLFWDGQDVIHFKKTIFSTLENDPLFARSY >ACOX3_seq3 MDEGIPDFPNGPLDIYRKKASFSWKDMMRFLEGDELIAFKQHVFRTLESDPLFARQPGEDVPVEQ

7. Slide 4 remember to annotate the source of the information 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.

8. Slide 5 remember to annotate the source of the information 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.