Question: gene prediction without GT-AG splice site bias
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gravatar for praasu
16 months ago by
praasu30
Prague, Czech republic
praasu30 wrote:

What would be the best approach to predict introns or gene model from RNA-seq/est and genome seq without GT-AG splice site rules?

ADD COMMENTlink modified 16 months ago by caggtaagtat1.3k • written 16 months ago by praasu30
1

Would you mind elaborating further on that rationale? U2 and U12 confer to a small class of dinucleotide pairs at the splice sites and are extremely well conserved from plants to animals. While there has been a very small number of non-consensus splice sites reported in the literature, many would agree that these variants are likely due to errors in annotations/interpretations, polymorphic difference between cDNA/genomic, or maybe pseudogene variants.

ADD REPLYlink modified 16 months ago • written 16 months ago by Eric Lim1.7k

There is a chance that some of the annotated non-consensus splice sites are due to error in annotation. However, there are several studies which suggests that non-canonical splice-sites really exist. I am working on the species where is possiblity that they have predominantly non-consensus splice site.

Some References, https://pubmed.ncbi.nlm.nih.gov/11058137-analysis-of-canonical-and-non-canonical-splice-sites-in-mammalian-genomes/

https://pubmed.ncbi.nlm.nih.gov/25123659-a-comprehensive-survey-of-non-canonical-splice-sites-in-the-human-transcriptome/

ADD REPLYlink written 10 months ago by praasu30
1
gravatar for caggtaagtat
16 months ago by
caggtaagtat1.3k
caggtaagtat1.3k wrote:

You could align your reads with STAR this directly gives you information about gaps in the alignment of your reads and therefor introns.

ADD COMMENTlink written 16 months ago by caggtaagtat1.3k
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