[Genome] Finding alternative terminal exons .......

[Rileen]

Hi,
       Thanks for that, I now have the list of all the exons in
UCSC genes with altFinish entries.

I just need to put this together with a table giving the info on gene
names/symbols, so that I know all the different transcripts of a
given gene, and can check for different terminal exons accordingly,
i.e something similar to the "refFlat" table for RefSeq data.

Thanks once again,
                                 Yours,
                                               Rileen

On 07/09/2007, Ann Zweig <ann at soe.ucsc.edu> wrote:
> Hello Rileen,
>
>         Thanks for the compliments on the browser.
>
>         You are correct that you are not going to find what you want directly
> from the altFinish items in the Alt Events track.  However, you can use
> that track as a starting point to get what you need.  Below I outline
> the steps you will need to take to find the ending exon for each transcript.
>
> 1. Make a custom track of the altFinish items from the Alt Events track.
>
> Navigate to the Table Browser ('Tables' from the top blue navigation
> bar) and create a custom track from the Alt Events track.  Be sure to
> configure the filter to include on altFinish items from the table:
> "name does match altFinish"
>
> Read more about creating custom tracks using the table browser here:
> http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#CustomTrack
>
>
> 2. Intersect that custom track with the UCSC Known Gene track (to make a
> new CT).
>
> Again, using the Table Browser, intersect the UCSC Genes track with your
> custom track from step 1.  Create a new custom track.  This will be a
> track containing all UCSC Genes that have overlap with altFinish items.
>
> Read more about doing intersections with the Table Browser here:
> http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection
>
>
> 3. Get the exons from the resulting track.
> Choose the resulting custom track from step 2 in the Table Browser.
> Choose BED as the output type.  From the next page, choose only the
> "Exons" button.  Press 'get BED'.  This will give you a list (in BED
> format) of each exon in each UCSC Gene from the custom track in step 2.
>
>
> 4. Mine the output for the location of the "last" exon.
> The BED output will have the following columns:
> chromosome
> chromStart
> chromEnd
> name
> score
> strand
>
> Here's an example of the 9 exons from one gene in the track:
>
> chr1    41748270        41749524        uc001cgz.1_exon_0_0_chr1_41748271_r     0       -
> chr1    41751073        41752008        uc001cgz.1_exon_1_0_chr1_41751074_r     0       -
> chr1    41756659        41756746        uc001cgz.1_exon_2_0_chr1_41756660_r     0       -
> chr1    41762992        41763168        uc001cgz.1_exon_3_0_chr1_41762993_r     0       -
> chr1    41813801        41813947        uc001cgz.1_exon_4_0_chr1_41813802_r     0       -
> chr1    41817994        41823576        uc001cgz.1_exon_5_0_chr1_41817995_r     0       -
> chr1    41867006        41867205        uc001cgz.1_exon_6_0_chr1_41867007_r     0       -
> chr1    41939173        41939253        uc001cgz.1_exon_7_0_chr1_41939174_r     0       -
> chr1    42156670        42156782        uc001cgz.1_exon_8_0_chr1_42156671_r     0       -
>
>         Here's how to interpret the name field:
>
> name: uc001cgz.1_exon_0_0_chr1_41748271_r
>
> uc001cgz.1      gene name
> exon            part of gene (all exon in your case)
> 0               exon number
> 0               score
> chr1            chromosome
> 41748271        chromStart
> r               strand (r = reverse, f = forward)
>
>         So, in the example above, there are 9 exons for gene uc001cgz.1.
> Because it is on the reverse strand, you want exon 0.  Conversely, if it
> were on the forward strand, you'd be looking for the exon with the
> highest number.
>
>         So, for this transcript, the location of the ending exon is:
> chr1:41748270-41749524
>
>
>         This should get you well on your way.  Be sure to write back to the
> list if you get stuck or need more direction.
>
>
> Regards,
>
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
>
>
>
> Rileen wrote:
> > Hi,
> >       Thanks once again for the great resource you provide :-)
> >
> > I've played around with the "knownAlt" track a bit, and was wondering
> > whether there's any simple way of deriving a list of alternative terminal
> > exons (ATEs) from it, or any other table/track. By this I mean instances
> > where the gene has transcripts ending in different exons, not merely
> > different positions in the same exon.
> >
> > For all the other events in the knownAlt track, the two positions seem
> > to provide useful information, but for the altFinish category, they always
> > seem to differ by 1.
> >
> > Why is this so?
> >
> > I was hoping that given the two positions, one cold check whether they
> > were in two
> > different exons to derive the list of ATEs as a subset of altFinish,
> > but that seems
> > wrong.
> >
> > Looking forward to your reply,
> >                                               Yours,
> >                                                              Rileen
> >
>


--
******************************************************************
"I know nothing, but i _know_ that."

Rileen Sinha                 rileen at yahoo.com
Personal Phone : (0049)3641412276   (cheaper to call)
                         (0049)17624078373
******************************************************************


-- 
******************************************************************
"I know nothing, but i _know_ that."

Rileen Sinha                 rileen at yahoo.com
Personal Phone : (0049)3641412276   (cheaper to call)
                         (0049)17624078373
******************************************************************