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Exploring the Sus scrofa (Pig) TRAF3 gene

  1. Find the TRAF3 (TNF receptor associated factor 3) gene in the pig reference, and go to the Gene tab.
    • Which strand of the genome is this gene located?
    • How many transcripts are there of the gene?
    • Which transcript produces the longest protein and how long is the protein sequence?

  2. What are some functions of TRAF3 according to the gene ontology (GO)? Have a look at the Ontologies pages for this gene.

  3. In the transcript table, click on the transcript ID for TRAF3-201, and to open the corresponding Transcript tab.
    • How many exons does it have?
    • Are any of the exons completely or partially untranslated?
    • Is there an associated sequence in UniProt? Have a look at the General identifiers for this transcript.

  4. Are there microarray (oligo) probes that can be used to monitor the expression of TRAF3-201?

  5. Now find the TRAF3 gene in the Berkshire pig breed.
    • Which strand of the genome is this gene located?
    • How many transcripts are there of the gene?
    • Which transcript produces the longest protein and how long is the protein sequence?
  6. How do the Ensmebl canonical transcripts differ between the pig reference and the Berkshire breed?
  1. Go to the Ensembl homepage. Select Pig from the drop-down list in the blue box, enter TRAF3 into the text box and click Go. In the search results page, click on Pig reference in the left-hand panel to restrict your results to the pig reference only. Click on the first hit TRAF3 (Pig Gene, Breed: reference) to open the Gene tab. Look at the Location section in the gene summary at the top of the page.

    The TRAF3 gene is located on the forward strand.

    Now look at the About this gene section in the gene summary at the top of the page.

    TRAF3 has 4 transcripts.

    Click on the Show transcript table button underneath the gene summary. Focus on the Protein column in the transcript table.

    The transcript ENSSSCT00000101908.1 (TRAF3-201) produces the longest protein at 573 amino acid residues in length.

  2. Gene Ontology maps terms to a protein in three classes: biological process, cellular component, and molecular function.

    Some of the GO terms associated to the TRAF3 gene are: regulation of cytokine production and proteolysis (biological process), protein kinase and metal ion binding (molecular function), and cytoplasm and endosome (cellular component).

  3. Click on ENSSSCT00000101908.1 in the transcript table. Under the summary information at the top of the page, focus on the About this transcript section.

    This transcript has 11 exons.

    Click on the Exons link in the left-hand side menu. In the Sequence column of the Exon table, look for any UnTranslated Regions (UTRs) which coloured in orange.

    Only exon 11 is partially untranslated. You can also see this in the cDNA view if you click on Sequence: cDNA in the left-hand menu.

    Click on External References: General identifiers in the left-hand menu. Look for UniProtKB in the External database column.

    A0A4X1TTD0.19 and A0A8W4FAU5.6 from UniProt match the translation of the Ensembl transcript. Click on the IDs to open the corresponding entry in UniProt.

  4. In the left-hand menu, look for External References: Oligo probes.

    The link is greyed out, which means that no commercial oligo probes are available to monitor expression of this transcript.

  5. Go to the Ensembl homepage by clicking on the Ensembl logo in the top left-hand corner of any page. Select Pig from the drop-down list in the blue box, enter TRAF3 into the text box and click Go. In the search results page, click on Pig berkshire in the left-hand panel to restrict your results to the Berkshire breed only. Click on the first hit TRAF3 (Pig Gene, Breed: berkshire) to open the Gene tab. Look at the Location section in the gene summary at the top of the page.

    The TRAF3 gene is located on the forward strand in the Berkshire breed.

    Now look at the About this gene section in the gene summary at the top of the page.

    TRAF3 has 5 transcripts in the Berkshire breed.

    Click on the Show transcript table button underneath the gene summary. Focus on the Protein column in the transcript table.

    The transcript ENSSSCT00065038580.1 (TRAF3-205) produces the longest protein at 573 amino acid residues in length.

  6. The Ensembl canonical transcript in the pig reference genome is 6,677 bases in length. The Ensembl canonical transcript in the Berkshire breed is 6,340 bases in length. This suggests that the TRAF3 Ensembl canonical transcript in the reference has more/larger UTRs compared to the Berkshire breed. To compare, you can open the Sequence: Exons pages in the Transcript tab in both breeds and look at the length of the UTR (coloured in orange).