Dear friends! I have a problem with finding those human genes that are transcribed by RNAP II. Do you have any ideas how to do this using UCSC or any alternative database? Thanks.
As far as I know there is no such database. That is mainly because the promoter structure of the core promoter is so variable and not well characterized. Experimental evidence is required (e.g. by ChIP-sequencing) because in-silico predictions are error prone. I found this recent article: http://www.ncbi.nlm.nih.gov/pubmed/20494980 that shows how an experimental analysis works. Have a look at Figure 2, there is a list of genes on chr 21 that have been investigated, that you could use as an example.
Search pubmed for "RNA polymerase II core promoter" reviews to get more articles.
What is mostly accepted about RNA-pol ii in short, maybe that helps to sort out the problem:
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[?] As soon as you get the gene listing you should be able to get their sequences through Ensembl or NCBI.[?]
+1 for finding a database with added value, however, from the user manual of epd: "Transcription by RNA POL II is bona fide assumed for protein coding genes but must be supported by alpha-amanitin data if the end product is an RNA." That's almost taking "RNA pol ii = messenger RNA = transcribes protein coding". The plus is that there might be few additional RNA genes.
This means in good confidence you can assume that all protein coding genes are transcribed by rna pol ii (+ few additional with verification).
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Thank you for your help!
Unfortunatly I don'have an access to the article you mentioned. Would you be so kind to send it to my mail? (nikulina.a.a@gmail.com).