Hello Lax, If I look at the record for NM_009717 in our tables I see all the same information you give below, and if I look at this item in the browser I do not see evidence for 3 exons, so it would seem that your command is working fine.
The exons for putative noncoding genes and untranslated regions are represented by relatively thin blocks, while those for coding open reading frames are thicker. In your example, the first "exon" (chr6:55627812-55629665) region incorporates the thin and thick areas in the left most block and the second "exon" (chr6:55630957-55631257) is the second block on the right. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu Lakshmanan Iyer wrote: > 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,exonEnd > s,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 > > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
