Transcript CARD9 - unipv

COURSE OF BIOINFORMATICS
2013-2014
Exam_30/01/2014
B
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Human ADAM22 gene
Slide 1
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1.
Report the Gene_ID, the chromosomal and genomic (in bp)
localization of the human ADAM22 gene
2.
How many different transcript isoforms exist for the ADAM22
gene? Do they differ in their starting point (i.e.: first exon)?
3.
Is the ADAM22 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 ADAM22 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 ADAM22
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 ADAM22 protein. Which
protein domains, if any, are reported and where are they localized?
8.
Could you find a murine homologue of the human ADAM22 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?
>ADAM22_seq1
FLLLCVLGTCPPARCGQAGDASLMELEKRKENRFVERQSIVPLRLIYRSGGEDESRHDALDTRVRGDLGG
PQLTHVDQAS
>ADAM22_seq2
FWLLCVLGTCPLARCGRAGVASLKGLERGKENRFLERQSIIPLRLIYRLGGEDETQHNQLDTRVRGDPGG
PQLTHVDKAS
>ADAM22_seq3
MIFCLLNTLRGISSKVERQWKLKEENIAIIREKLEETQYHLLPCQHAMDYSGMFYDGNHTYLIEPDENYT
SDDDFHFHS
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
ADAM22 gene? Recontruct the ontology of the GO terms in each of
the three categories in which the ADAM22 gene is annotated.
Slide 5
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12. In the ADAM22 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.