1. COURSE OF BIOINFORMATICS 2013-2014 Exam_31/01/2014 A

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

3. Human ABCB7 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 ABCB7 gene 2.How many different transcript isoforms exist for the ABCB7 gene? Do they differ in their ending point (i.e.: last exon) or in their starting point (i.e.: first exon)? 3.Is the ABCB7 gene involved in the etiology of any disorders? If yes, annotate disorder name and the corresponding MIM number 1.Which are the genes contained in the genomic region spanning 200 kb upstream and 200 kb downstream to the ABCB7 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 around the first exon of the ABCB7 gene (i.e. about 5kb), could you identify putative binding sites for transcriptional factors identified by ChIP experiments? Is there any putative binding sites for transcriptional factors identified by different experiments? If yes, report the name of the transcription factor and its binding position. 6.In your opinion, are there evidences of other transcriptional regulatory elements in the same genomic region? 7.Report the Accession code of the reviewed ABCB7 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 comparison between the sequence of the protein encoded by the human ABCB7 gene and the sequence of the mouse homologous protein. Report the percentage of identities and of positives. Do the same between the human and the Drosophila melanogaster proteins. 9.Do a Multiple Sequence Alignment (suggestion: use ClustalW2) with the human, mouse and Drosophila 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.

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 ABCB7 gene? Recontruct the ontology of the GO terms in each of the three categories in which the ABCB7 gene is annotated.

8. Slide 5 remember to annotate the source of the information 12.In the ABCB7 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.