[Genome] 3'utr coordinates from the table browser

[Brooke Rhead]

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	+
> 
> 
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