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Exploring the MYH9 gene in human

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Exploring the MYH9 gene in human

  1. In Ensembl, find the human MYH9 (myosin, heavy chain 9, non-muscle) gene and open the Gene tab.
    • On which chromosome and which strand of the genome is this gene located?
    • How many transcripts (splice variants) are there and how many are protein coding?
    • What is the longest protein-coding transcript, and how long is the protein it encodes?
    • Which transcript would you take forward for further study?

  2. Click on Phenotypes at the left side of the page. Are there any diseases associated with this gene, according to Mendelian Inheritance in Man (MIM)?

  3. What are some functions of MYH9 according to the Gene Ontology (GO) consortium? Have a look at the GO: Biological process pages for this gene.

  4. In the transcript table, click on the transcript ID for MYH9-201, and go to the Transcript tab.
    • How many exons does it have?
    • Are any of the exons completely or partially untranslated?
    • Is there an associated sequence in UniProtKB/Swiss-Prot? Have a look at the General identifiers for this transcript.
  5. Are there microarray (oligo) probes that can be used to monitor ENST00000216181 expression?
  1. Select Human from the Species drop-down list and type MYH9. Click Go. Click on MYH9 (Human Gene) in the search results which will send you to the Gene tab.
    • The gene is located on chromosome 22 on the reverse strand.
    • Ensembl has 23 transcripts annotated for this gene, of which 6 are protein-coding.
    • The longest protein-coding transcript is MYH9-215 and it codes for a protein that is 1,981 amino acids long.
    • MYH9-201 is the transcript I would take forward for further study, as it is the MANE Select transcript (for a description, mouse-over the MANE Select flag in the transcript table).
  2. Click on Phenotypes in the left-hand panel to see the associated phenotypes. There is a large table of phenotypes. To see only the ones from MIM, type MIM into the filter box at the top right-hand corner of the table.

    These are some of the phenotypes associated with MYH9 according to MIM: Deafness, Autosomal dominant 17 and Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss. You can click on the records for more information.

  3. The Gene Ontology project maps terms to a protein in three classes: biological process, cellular component, and molecular function. Click on GO: Biological process on the left-hand panel. Angiogenesis, cell adhesion, and protein transport are some of the roles associated with MYH9. All GO terms are associated with a single transcript: ENST00000216181.

  4. Click on ENST00000216181.11 in the transcript table. You should now be on the Transcript tab.
    • It has 41 exons, shown in the Transcript summary.

    Click on the Exons link in the left-hand panel.

    • Exon 1 is completely untranslated, and exons 2 and 41 are partially untranslated (UTR sequence is shown in orange). You can also see this in the cDNA view if you click on the cDNA link in the left side menu.

    Click on General identifiers in the left-hand panel.

    • P35579.247 from UniProt/Swiss-Prot matches the translation of the Ensembl transcript. Click on P35579.247 to go to UniProtKB, or click align for the alignment.
  5. Click on Oligo probes in the left-hand panel.

    Probesets from Affymetrix, Agilent, Codelink, Illumina, and Phalanx OneArray match to this transcript sequence. Expression analysis with any of these probesets would reveal information about the transcript. Hint: this information can sometimes be found in the [ArrayExpress Atlas] (https://www.ebi.ac.uk/biostudies/arrayexpress).