how to find out whole gene sequence with promoter, exon and intron organization using your genome browser.

[Irudayam, Maria Johnson]

Hi, how to find out whole gene sequence with promoter, exon and intron organization using your genome browser. I am trying for the gene called “inhibin beta A”. Thanks. Regards, Johnson,

 

[Matthew Speir]

Hi Johnson,

Thank you for your question about obtaining gene sequences from the UCSC Genome Browser.

Here is a link to the INHBA gene in the human genome assembly hg38/GRCh38: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=mspeir&hgS_otherUserSessionName=hg38_MLQ_INHBA. From there I will provide you some steps to obtain the sequence for the INHBA (inhibin beta A) gene, including some number of bases upstream of this gene:

1. Click on the INHBA gene in the display (the name should be highlighted by a black box).
2. Under the section titled "Sequence and Links to Tools and Databases", click the "Genomic Sequence" link.
3. Under "Sequence Retrieval Region Options", check the boxes for 5' UTR exons, CDS exons, 3' UTR exons, and Introns. Additionally, check the box for "Promoter/Upstream by" and enter the number of bases you want upstream of your gene. Lastly, click the button for "One FASTA record per gene".
4. Under "Sequence Formatting Options", click the button for "Exons in upper case, everything else in lower case."
5. Click "submit".

From the page I linked going to the INHBA location in the genome, you can search for other gene names or gene symbols (e.g. SOD1) to see more genes and download their sequences using the same steps described above.

If you are new to the UCSC Genome Browser, I would highly encourage that you look at some of the training documentation we provide: http://genome.ucsc.edu/training/index.html. I would recommend starting with the Open Helix videos: http://www.openhelix.com/ucsc.

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.

Matthew Speir
UCSC Genome Bioinformatics Group

On 9/29/17 2:16 PM, Irudayam, Maria Johnson wrote:

Hi, how to find out whole gene sequence with promoter, exon and intron organization using your genome browser. I am trying for the gene called “inhibin beta A”. Thanks. Regards, Johnson,

 

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[Irudayam, Maria Johnson]

Thank you very much. Your info is highly useful. Thanks for the time and help. Regards, Johnson