mrna length for some genes

[Varun Gupta]

Hi,

I have a list of genes and i want to find their mrna length.

For example lets take MRPL10
http://genome.ucsc.edu/cgi-bin/hgc?hgsid=355060111&c=chr17&o=45900637&t=45908907&g=refGene&i=NM_148887

If you see the mrna size is 1847.

I want to extract these sizes for all the genes together.

Can you tell me how

Thanks

Regards
Varun

[Luvina Guruvadoo]

Hi Varun,

Thanks for your question. You can use the Table Browser to retrieve this data from the appropriate table, but once you have this information, you will need to do some calculations to get the actual lengths. You can do this using your own tools, or you may be interested in Galaxy: http://main.g2.bx.psu.edu/ . Galaxy is a site run by Penn State that works in conjunction with the UCSC Genome Browser.  They have tools that will perform calculations on columns in a table.  If you need help with Galaxy, their contact information can be found here: http://wiki.galaxyproject.org/Support.

Using the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables), make the following selections:

clade: Mammal
genome: Human
assembly: hg19
group: Genes and Gene prediction Tracks
track: RefSeq Genes
table: refGene
identifiers: paste or upload a list of IDs
output format: selected fields from primary and related tables

After clicking on "get output", select the fields in which you are interested from hg19.refGene. Once you have these values from the table, you can calculate the lengths you need.

The length of a gene (including introns) is txEnd - txStart. The total length of all the exons in a gene (mRNA length) will be the sum of each of the exonEnds - exonStarts (the number of exons is listed in the field 'exonCount').

I hope this information is useful and answers your question. 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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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