Exploring the human MYH9 gene
(a) Find the human MYH9 (myosin, heavy chain 9, non-muscle) gene, and go to 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 transcript, and how long is the protein it encodes?
- Which transcript would you take forward for further study?
(b) Click on Phenotypes at the left side of the page. Are there any diseases associated with this gene, according to MIM (Mendelian Inheritance in Man)?
(c) What are some functions of MYH9 according to the Gene Ontology consortium? Have a look at the GO pages for this gene.
(d) 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.
(e) Are there microarray (oligo) probes that can be used to monitor ENST00000216181 expression?
(a) Go to the Ensembl homepage (http://www.ensembl.org).
Select Search: Human and type MYH9. Click Go.
Click on either the Ensembl ID ENSG00000100345 or the HGNC official gene name MYH9.
- Chromosome 22 on the reverse strand.
- Ensembl has 11 transcripts annotated for this gene, of which three are protein coding.
- The longest transcript is MYH9-201 and it codes for a protein of 1,960 amino acids
- MYH9-201 is the transcript I would take forward for further study, as it is the MANE Select.
(b) Click on Phenotypes at the left 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 of the table.
These are some of the phenotypes associated with MYH9 according to MIM: autosomal dominant deafness and Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss. Click on the records for more information.
(c) > The Gene Ontology project (http://www.geneontology.org/) maps terms to a protein in three classes: biological process, cellular component, and molecular function. Meiotic spindle organisation, cell morphogenesis, and cytokinesis are some of the roles associated with MYH9.
(d) Click on ENST00000216181.11
- It has 41 exons, shown in the Transcript summary.
Click on the Exons link in this side menu.
- 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.
- P35579-1 from UniProt/Swiss-Prot matches the translation of the Ensembl transcript. Click on P35579-1 to go to UniProtKB, or click align for the alignment.
(e) Click on Oligo probes in the side menu.
Probesets from Affymetrix, Agilent, Codelink, Illumina, and Phalanx 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: www.ebi.ac.uk/arrayexpress/