[Genome] downloaded exons

[Kayla Smith]

Hello Chris,

This is best described with an example.  I shall choose the "CITED2" 
gene on the hg18 assembly.  For your reference, this gene is at this 
position: chr6:139,735,090-139,737,478.  Please note that this gene is 
on the reverse strand, which you can see from the <<< arrows on the 
display of the gene.

Once I have this gene in view in the Genome Browser, I click on "Tables" 
to go to the Table Browser.  I use the following settings:

clade: Vertebrate;  genome: Human; assembly: Mar. 2006
group: Genes and Gene Prediction Tracks;  track: UCSC Genes;
table: knownGene; position: chr6:139,735,090-139,737,478
output format:  BED.

Click "Get output" and on the next page select the radio button next to 
"Exons", and click "Get BED".

Here are the 2 lines of output:

chr6    139735089    139736782    uc003qip.1_exon_0_0_chr6_139735090_r 
   0    -
chr6    139737242    139737478    uc003qip.1_exon_1_0_chr6_139737243_r 
   0    -


Looking at: uc003qip.1_exon_0_0_chr6_139735090_r

Here we have:

1.  uc003qip.1 is the name of the UCSC gene
2.  exon_0_0 is the number of the exon.  You'll note that the next exon 
is labeled "exon_1_0".
3.  chr6_139735090 is the starting position of that exon
4.  r means "reverse strand"

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

Kayla Smith
UCSC Genome Bioinformatics Group



Chris Zaleski wrote:
> Greetings,
> 
> I have a question about downloaded BED files from the table browser. I've
> chosen a 'Gene' track, BED output format, and then Exons (from the 2nd
> page). An example 'name' field looks like the following:
> 
> NM_152486_exon_0_0_chr1_850984_f
> 
> I understand most, but not all, of the tokens in this string. Could you
> please explain what all the items represent?
> 
> Thanks very much,
> Chris Zaleski
> Bioinformatics Team Lead
> Tenenbaum Lab - SUNY Albany
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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