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EndFragment:0000001662 StartSelection:0000000199 EndSelection:0000001662 I
have a gene with the following structure:
5' uuuuuEEEEEEuuuu>>>>xxxxx 3'
Where u stands for UTR region and E for exon.
So, I have a 3'UTR with two exons. However, when I use the following command
to get the coordinate information:
k=`mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N \
-e 'select
name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds,id,name2,cdsStartStat,cdsEndStat
from refGene where name2 ="'${I}'";' mm9`
For a gene named: Neurod6, I get
NM_009717 chr6 - 55627812 55631257 55628630 55629644 2 55627812,55630957,
55629665,55631257, 125408 Neurod6 cmpl cmp
I get only 2 exon and two exon start sites where as I know that there are 3
exons when I see the RefSeq gene on UCSC track.
How can I get all the three exon start sites?
In general, give a number of gene names, how can I get the coordinates of
all exons including UTRs for the gene.
I know that I can do it in a round about way with Table browser but I want
to avoid interactive session. I would rather have a mysql query script to do
it automatically for multiple gene lists.
-Best
-Lax
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