Download CARD9

COURSE OF BIOINFORMATICS
2013-2014
Exam_31/01/2014
A
Insert the requested information:
• Name and Surname:
• Matricula Number:
• E-mail address:
(I will contact you at this address!!)
Human ABCB7 gene
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.
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.
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.
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.
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.