Question: How Can I Find 1-And 2-Exone Genes?
3
gravatar for nikulina
8.8 years ago by
nikulina280
Cambridge
nikulina280 wrote:

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!

exon ucsc • 1.3k views
ADD COMMENTlink modified 8.0 years ago by Pierre Lindenbaum118k • written 8.8 years ago by nikulina280
4
gravatar for Pierre Lindenbaum
8.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

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; }'
ADD COMMENTlink modified 6 months ago by RamRS20k • written 8.8 years ago by Pierre Lindenbaum118k

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

ADD REPLYlink written 8.8 years ago by Pierre Lindenbaum118k

thank you so much :)

ADD REPLYlink written 8.8 years ago by nikulina280
3
gravatar for Giovanni M Dall'Olio
8.8 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

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

ADD COMMENTlink written 8.8 years ago by Giovanni M Dall'Olio26k

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?

ADD REPLYlink written 8.8 years ago by nikulina280

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.

ADD REPLYlink written 8.8 years ago by Giovanni M Dall'Olio26k

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 :)

ADD REPLYlink written 8.8 years ago by nikulina280
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