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How Can I Find 1-And 2-Exone Genes?

Dear friends! I have to find in UCSC human genes that are transcribed by RNAP II and contain only 1 or 2 exons. Would you be so kind to help me to cope with this problem. Thanks!

ucsc exon
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by nikulina nikulina

2 answers

Same as giovanni but from the command line:

curl "http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/knownGene.txt.gz" |\
 gunzip -c |\
 awk -F '     ' '{if($8=="1" || $8=="2") print; }'
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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

btw, sorry: I've no idea about getting the information about the RNAPII....

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written by Pierre Lindenbaum Pierre Lindenbaum

thank you so much :)

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written by nikulina nikulina

It's very simple: go to UCSC-Table browser and select the table 'Known Genes'. on the same page, click on 'Filters' and you will arrive to a form where you can select genes which have a range of # of exons of your choice.

alt text

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written by Giovanni M Dall'Olio Giovanni M Dall'Olio

Thank you so much! I got them. One more thing is the way to specify my query for genes that are transcribed by pol II only. Are there special filters to do this?

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written by nikulina nikulina

I don't know of any database with that kind of information, sorry :( you should better open a new question to ask if someone knows of a database for genes transcribed by polII, you will be more likely to get answers.

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written by Giovanni M Dall'Olio Giovanni M Dall'Olio

Thank you for your interest. I think I can write some perl script to sort the genes according to the presence of specific binding sites for RNAP II. And it is a good idea to set up a new question anymore :)

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written by nikulina nikulina

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