[Genome] 3'utr coordinates from the table browser

[Brooke Rhead]

Hi Wen,

I finally have an explanation for you about the second "0" in the Table 
Browser output headers (your question #2 below):

http://www.soe.ucsc.edu/pipermail/genome/2008-March/015765.html

Thanks for being patient!

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Brooke Rhead wrote:
> Hello Wen,
> 
> Please see answers to your questions intersperesed below:
> 
> Wen Huang wrote:
>> Hi,
>>
>> I have a few questions about the BED file generated when retrieving  
>> 3'utr coordinates.
>>
>> I choose 3'UTR exons from the output.
>>
>> Below are a few lines from the file. I have a few questions:
>>
>> 1) since these are 3'UTR exons (not just 3'UTR), do they also include  
>> some exon sequences that are from the coding region? (e.g. STOP in the  
>> middle of a exon) For 3'UTRs that span multiple exons, are all the  
>> exons included?
> 
> The UTRs are the untranslated regions of exons.  They do not include 
> coding regions.  For UTRs that span multiple exons, all exons are 
> included in the Table Browser output, but multiple exons will occupy 
> multiple lines in the BED file.
> 
> An easy way to examine the regions output by the Table Browser is to 
> choose "custom track" as the output format -- the selected regions will 
> appear in a "user track" at the top of the Genome Browser display.
> 
>> 2) the first three and the last columns are easy to understand,  
>> correct me if I am wrong. chromosome id, start, end, strand. What do  
>> the numbers in, for example, "NM_174812_utr3_0_0_chr16_3833_r" mean  
>> and what does the second column from the last mean?(they are all 0's).
> 
> I think the second zero in the name generated by the Table Browser is 
> unused in this instance, but I am not certain.  I have asked our 
> developers about it, and I will send a follow-up to this answer when I 
> know for sure.
> 
>> 3) are these coordinates start from 0 or 1?
> 
> The BED coordinates start from 0.  See an explanation here:
> http://genome.ucsc.edu/FAQ/FAQtracks#tracks1
> 
> I hope this information is helpful.
> 
> --
> Brooke Rhead
> UCSC Genome Bioinformatics Group
> 
> 
> 
>> Thank you very much.
>>
>> Wen
>> chr16	3882	5634	NM_174812_utr3_0_0_chr16_3883_r	0	-
>> chr16	35447	35625	NM_001080309_utr3_1_0_chr16_35448_f	0	+
>> chr16	71582	72004	NM_001098464_utr3_4_0_chr16_71583_f	0	+
>> chr16	191157	192344	NM_174143_utr3_10_0_chr16_191158_f	0	+
>> chr16	354114	354322	NM_174088_utr3_4_0_chr16_354115_f	0	+
>>
>>
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome