Longest known Isoform Refseq for human

[Adrian Johnson]

Dear UCSC genome browser staff,

I am looking to obtain the human RefSeq ID for longest known isoform (
or even canonical isoform). How could I get that list.

Or more specifically:

1. I want to obtain GTF file for introns of longest known isoform. I
dont know how to pull this from UCSC. It will make my day, if I could
get this :-)

Could you please help.

thanks
Adrian

[Brian Lee]

Dear Adrian,

Thank you for using the UCSC Genome Browser and your question about the longest isoform for RefSeq for human.

You would likely be interested in this summary webpage we have created about the gene sets: http://genomewiki.ucsc.edu/index.php/Gene_Set_Summary_Statistics

You can also extract these kinds of queries from the underlying data tables either using MySQL (http://genome.ucsc.edu/goldenPath/help/mysql.html) or using our Table Browser.

For example, if you went to the human hg19 database on the Table Browser, you could set the "group:" to "Genes and Gene Predictions" and then the "track:" to "RefSeq Genes" and then the table would select refGene. Then you could click the "filter:create" button and in the "Free-form query:" section you could paste a version of the following and then click "submit": 

txEnd-txStart >= 2320000

This will request all transcripts that have size greater than 2,320,000 bp between transcription start and end. You could press "get output" at this point and you would receive genePred output from the refGene table for matching transcripts (2 in this case for NBPF20 and NBPF19).

Or you could change the output to "GTF" and then click "get output", however the result will not be in a limited GTF format. Here is a link to a session with this filter in place: http://genome.ucsc.edu/cgi-bin/hgTables?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg19_longRefSeqFilter

To learn more on how to use our genePred format to make better GTF output, please see this FAQ: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download37

Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further questions and reply to gen...@soe.ucsc.edu messages will be archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UC Santa Cruz Genomics Institute

Training videos & resources: http://genome.ucsc.edu/training/index.html

Want to share the Browser with colleagues?

Host a workshop: http://bit.ly/ucscTraining

Adrian

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