Understanding exomic fields

[tmkas]

Hi all,

I got some WGS data in excel files, now I want to extract the exome from this data. There is one filter option called region which contains the following fields

exonic
splicing
ncRNA
UTR5
UTR3
intronic
upstream
downstream
intergenic
etc.

I'm confusing here which fields are the exomic part and which are non coding? Is there anybody who can help?

[sciencewu]

exonic , UTR5 and UTR3

[tmkas]

thanks but what about following regions:

exonic;splicing
ncRNA_exonic
ncRNA_UTR3
ncRNA_UTR5

[sciencewu]

I think splicing not including in the region of exome. also this can affect the function of protein. ncRNA is also the regulation element of genomic region.
this is my opinion, how do you think?

[JamieHeather]

ncRNA = non coding RNA

[tmkas]

I mean whether these are included in the exome or not?

[tmkas]

Can anyone say anything more?

[JamieHeather]

You might need to supply more information. What is your data the output of? Have you checked the documentation to see what they say about all the different field options?

That said, the clue was in the name somewhat. Non-coding RNAs don't encode protein, so I doubt you would want to include those in the exome (although I appreciate the terms are all open to a bit of wiggle room).

[tmkas]

Following are the fields into which whole genome data is covered from which i need to take out the exome. Which fields below cover the exome part of the genome?

exonic
splicing
ncRNA
UTR5
UTR3
intronic
upstream
downstream
intergenic
exonic;splicing
ncRNA_exonic
ncRNA_UTR3
ncRNA_UTR5