Exome location query
Guevarra, Ma Carmela B.
I hope this email finds you well. I would like to inquire about how to find an exon location using the USCS genome browser. I have watched some of the youtube tutorials however it was 8 years ago and they were using the outdated version. Also, would there be an upcoming training program? thank you very much.
Kind regards,
Mela
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Gerardo Perez
Hello, Mela.
Thank you for your interest in the UCSC Genome Browser and for sending your inquiry.
You can use the Table Browser to get the exon locations for a gene or list of genes. The gene name would have to match the gene names in a gene track. You would have to select a gene track dataset to extract the exon data. Here are two gene tracks that we offer for human hg38/hg19 and mouse mm10/mm39:
NCBI RefSeq: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite&position=default
GENCODE: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=knownGene&position=default
The following FAQ entry can explain the differences between the NCBI RefSeq and GENCODE tracks: https://genome.ucsc.edu/FAQ/FAQgenes.html#ensRefseq
As an example, you can do the following to get the exon locations from the hg38 GENCODE V44 track by using a list of gene names:
1. Navigate to the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) and make the following selections:
clade: Mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)
group: Genes and Gene Predictions
track: GENCODE V44
table: knownGene
2. Set the region to “genome”
3. Click "paste list" or "upload list" next to identifiers (names/accessions): and enter/upload a list of gene names such as the following and then click "submit":
6. Insert a name next to “output filename”
7. Set the output format to “Selected fields from primary and related tables”. This will allow you to select fields of interest. Click "get output"
8. Select “name”, “chrom”, “exonStarts”, “exonEnds”, and other fields of interest. These fields will give you the gene name and exon locations in the genome for the genes
6. Click “get output”
The output will then give you the exon locations for the list of genes.
For more information on using the Table Browser, please review the Table Browser User Guide:
https://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
One way to get the exon location from the browser graphic display for hg38 would be by right-clicking on the exon for the NCBI RefSeq Track. You will see the “Zoom to exon” option. This option will take you to the location for the exon on the browser graphic.
As for your question about an upcoming training program, unfortunately; we do not have an upcoming UCSC Genome Browser training scheduled.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Gerardo Perez
UCSC Genomics Institute
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Guevarra, Ma Carmela B.
Thank you so much for your help. I was able to look for the exon.
Sincerely,
Mela
Sent: Wednesday, October 11, 2023 12:09 PM
To: Guevarra, Ma Carmela B. <mgue...@meei.harvard.edu>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] Exome location query
External Email - Use Caution
Matthew Speir
You can open bigBed/bb files using the utility bigBedToBed:
Additionally, if you're interested in a specific subset of SNPs, you can find info about downloading the different subsets here: https://genome.ucsc.edu/FAQ/FAQdownloads.html#snp. (It uses dbSnp153 as an example, but it's easy to change the URLs to point to dbSnp155 files.)
Matthew Speir
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/DM6PR04MB5737284F2DE453A66D7CE07F9CA0A%40DM6PR04MB5737.namprd04.prod.outlook.com.