Identification of 3'UTR of a gene not yet discovered in pig

Question

[ChIP]

Hi All,

I need to find out a 3'UTR region of a gene (ITPR2), that is very well documented in human and rat but not in pig. I am not sure about the approach that I should adopt to discover this region in pig. I have RNA-seq dat for pig, in case that helps.

Could anyone please walk me through the steps or possible steps to identify this region.

Thank you in advance.

[Satyajeet Khare]

If the 3' UTR of the gene of your interest is not annotated already, you can perform sequence alignment (Tophat or Hisat) followed by transcript prediction (Cufflinks). Or you can perform 3'RACE in lab to detect 3' end of the transcript.

[ChIP]

Hi Satya,

My apologies in advance for my limited knowledge in this area and the for the following question, the gene itself has not been annotated in pig and if I am correct you are advising for Transcript alignment with TopHat or STAR followed by transcript prediction, right?

[Satyajeet Khare]

Yes, transcriptome alignment and transcript prediction along with Blatting annotated UTR sequence in Pig genome should be good enough.

[microfuge]

There seems to be orthologs/paralogs for this gene in pigs in ensembl . I might be wrong but just in case.

Answer 1

[WouterDeCoster]

Was your RNA-seq performed using polyA enrichment? In that case you are relatively sure about the end of the transcript, and you need to search for the in-frame stop codon.

In addition, you could compare how well conserved the UTR is between rat and human. That could give you an idea whether you can just extrapolate those UTR annotation to pig, by e.g. blatting the sequence.

[ChIP]

Hi,

I should map the RNA-seq data using TopHat and use cufflinks for transcript prediction?

Answer 2

[EVR]

hi

Try to find the CDS(ATG and TAA,TAG,TGA) region in the gene of your interest in pig. The region preceding to CDS region(ATG) in 5'UTR and region after CDS region(TAA,TAG,TGA) is 3'UTR