Exploring the dog DTHD1 gene
(a) Find the dog DTHD1 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?
(b) In the transcript table, click on the transcript ID for DTHD1-202, 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. (d) Are there microarray (oligo) probes that can be used to monitor ENSCAFT00000049095 expression?
(a) Go to the Ensembl homepage.
Select Search: Dog and type DTHD1. Click Go.
Click on either the Ensembl ID ENSCAFG00000016290 or the VGNC official gene name DTHD1.
- Chromosome 3 on the reverse strand.
- Ensembl has two transcripts annotated for this gene, of which both are protein coding.
- The longest transcript is DTHD1-202 and it codes for a protein of 904 amino acids.
(b) Click on ENSCAFT00000049095
It has 10 exons. This is shown in the Transcript summary or in the left hand side menu Exons.
Click on the Exons link in this side menu.
Exon 10 is partially untranslated (UTR sequence is shown in red). You can also see this in the cDNA view if you click on the cDNA link in the left side menu.
J9NUJ5 from UniProt/Swiss-Prot matches the translation of the Ensembl transcript. Click on J9NUJ5 to go to UniProtKB, or click align for the alignment.
(c) Click on Oligo probes in the side menu.
The AFFY Canine_2 probeset from Affymetrix 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/
