Mouse zinc finger protein
The Zinc finger protein 746 (Zfp746) gene belongs to the krueppel C2H2-type zinc-finger protein family, which represents the best-characterised class of zinc fingers and are very common mammalian transcription factors.
(a) Search for the Zfp746 gene in mouse. What is the genomic location of the Zfp746 gene? How many transcripts does this gene have?
(b) Export the exon sequences of Zfp746 and display them as HTML.
(c) Export the genomic sequence of the region and capture 1000bp upstream and downstream; display as HTML.
(d) Go to the Orthologues page. What is the Ensembl gene ID of the human orthologue? Display the mouse and human protein alignment. How large in amino acids is the human protein? Display the mouse and human cDNA alignment.
(a) The gene is found on chromosome 6 and the gene has seven transcripts.
(b) Click on Export data, which you can find on the left of the page.
Click on the drop down menu next to Genomic and select None, as a result, genomic sequence will NOT be displayed. Now de-select all other options for FASTA except Exons and click Next. Select to display the output as HTML. Exon sequences should now be displayed in a new window.
There are a range of different outputs you can choose to download, in addition to FASTA, such as GFF3 and CSV. You can also choose to display the information as a text file or Compressed text (.gz) file. You can also export data under the location and transcript tabs.
(c) Click on Export data again. Type 1000 in the 5’ and 3’ Flanking sequence fields. Click on the drop down menu next to Genomic and select Unmasked. Now de-select all other options for FASTA and click Next. Select to display the output as HTML.
The unmasked genomic sequence with 1000bp upstream & downstream should now be displayed in a new window.
(d) Click on Orthologues found on the left of the page and scroll down to view the Human orthologue.
The Ensembl gene ID of the human orthologue is ENSG00000181220.
Click on Alignment (protein), which you can find underneath the human Ensembl gene ID. By default, this will display the protein alignment between mouse and human and provides the number of amino acids for each protein.
The human protein consists of 652 aa.
Now click on Alignment (cDNA). The alignment between mouse and human cDNA should now be displayed.