[Genome] (no subject)

[Jim Kent]

Hi Steve - It's good to see you using the new gene set.

* In the kgTxInfo table, there's a category called nearCoding. Does that
mean it's noncoding but located near a coding sequence?

This page has info on the kgTxInfo table fields.
     http://hgwdev.cse.ucsc.edu/cgi-bin/hgGene? 
hgg_do_txInfoDescription=1
This table will be part of the gene details page next week.  See
also the table browser schema.  You can get this by following the tables
link, selecting "all tables" from group, and then scrolling through the
list of tables until you find kgTxInfo, and then hitting the  
"describe table
schema" button.


* What's the difference between knownAlt and knownIsoforms? knownAlt  
appears
to link up with the kgProtMap and kgProtMap2 tables via the bin field.

Known Isoforms just clusters together overlapping transcripts.  Known  
alt
enumerates various alt-splicing and related events in the UCSC genes  
set.
The bin field is just to speed queries.  It is only related at the  
database level
to other tables via the chromosome position fields.   See also the  
Table Browser
schema page for these two tables.

Take care,
	Jim