Analysing conserved domains, motifs, diseases and chemicals associated with ADARB2 Gene in Homo sapiens

Adenosine deaminase, RNA-specific, B2 (RED2 homolog rat), also known as ADARB2, is a human gene. RNA-editing deaminase-2 (RED2, or ADARB2) is a member of the double-stranded RNA (dsRNA) adenosine deaminase family of RNA-editing enzymes. Adenosine deamination of pre-mRNA results in a change in the amino acid sequence of the gene product, which differs from that predicted by the genomic DNA sequence.[1]

Following are the steps required in this search.

First go to PANTHER (Protein ANalysis THrough Evolutionary Relationships) and click on keyword search.

Enter ADARB2 in the search field and click on Genes under PANTHER DATABASES category.

Click on NCBI: H.Sapiens in Species Filter category to narrow down your search of ADAR Genes only in Homo sapiens.

In the Panther Gene List click on GeneID:105 and the associated link to view the subfamily information, classification and also the proteins related to this gene in which we are interested.

Click on the protein link below which will display a page having the protein sequence; copy it.

Now open NCBI Conserved Domain Database CDD.

Paste your protein sequence in the box, select CDD in the scroll down menu and submit your query.

On submitting your query following page will be displayed having conserved domains of our protein having accession number NP_061172.

Click on the link DSRM (Double-stranded RNA binding motif) to view the details of the conserved domain in this case cd00048 including its sequence cluster. You can also view the structure with Cn3D by clicking on the link.

Open KEGG GENES Database and click on GENES in the GENE catalogue.

In the text field type ADARB2 to find its accession number in Homo sapiens.

The following page will be displayed having our required gene accession number; click on it.

The following page having detailed information about this gene will be displayed on clicking the link shown. Now click on Paralog link.

By clicking on paralog it will return 197 hits. Select operation ‘Search common motifs’ and click select. Perform this operation on first ten entries.

Following are the two result pages.

Now in the end in order to find the human diseases associated with this gene and also the chemicals that interact with this gene we will go to CTD: The Comparative Toxicogenomics Database.When the page opens perform keyword search.

Select Genes in the scroll down menu and type ADARB2 in the search field and click on search.

The following page will be displayed having the basic information about this gene.

Click on Diseases in the menu shown below to find out which disease(s) is associated with this gene.

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The above result page shows that inflammation is related to this gene. Now click on the link Chemicals in the main menu to find out their interaction with this gene.

Doing so will give us the following results.

So we see that Flavonoids is the interacting chemical in this case.

REFERENCES:

[1] http://en.wikipedia.org/wiki/ADARB2

Contributed by:Sania Shamim Khan