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

Question

[nikulina]

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!

Answer 1

[Pierre Lindenbaum]

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; }'

[Pierre Lindenbaum]

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

[nikulina]

thank you so much :)

Answer 2

[Giovanni M Dall'Olio]

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.

[nikulina]

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?

[Giovanni M Dall'Olio]

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.

[nikulina]

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 :)