[Genome] Overlap between refSeq, known_gene and all_mRNA tables

[Kayla Smith]

Alessandro,

The Known Genes details page has information on how it is created.  Look 
in the "Methods" section.  Here is a link:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=knownGene

Q1.) No, not all refGene sequences are contained in knownGene.  Here is 
a link to a previously answered mailinglist question on that topic:
http://www.cse.ucsc.edu/pipermail/genome/2006-November/012041.html

Q2.)Of the two table combinations you mention, all_mrna and refGene 
would cover more of the genome.

I hope this is helpful to you.  Please don't hesitate to contact us 
again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group

Alessandro Guffanti wrote:
> Dear Genome support:
> 
> I would like to know which is the extent of overlap between the following
> UCSC db tables:
> 
> knownGene
> all_mrna
> refGene
> 
> I understand that RefSeq sequences are NOT included in all_mrna:
> 
> mysql> select * from all_mrna where qName LIKE 'NM_%';
> Empty set (0.00 sec)
> 
> Q1) are all the refGene sequences contained in knwonGene ?
> Q2) to obtain the total coverage of the human genome in terms of 
> (redundant) transcripts, shall I query
> all_mrna AND refGene ? or all_mrna and knownGene ?
> 
> Best wishes and thanks in advance,
> 
> Alessandro G
>