Lots of exons in Mitranscriptome file couldn't be found in Enssembl browser.

[Hua Zhong]

Hi all,

I tried to browse the transcripts in Mitranscriptome gtf file on Enssembl browser. But lots of the exons couldn't match any known exons. Even though lots of other exons could find matches, the coordinates were different. Is there anything wrong with the coordinates of the transcripts in Mitranscriptome? I checked, both of Mitranscriptome and Enssembl use GRCh 37 human genome as the reference.

Hua

[Yashar Niknafs]

Hello Hua,

As you can see in our manuscript, we find fairly good exonic overlap with annotated transcriptomes, but we also find a lot of novel exons. One place we struggle in particular is identifying transcriptional stop sites. So you'll notice the MiTranscriptome has long last exons. This is a challenging part of assembly and something we are working on. Otherwise, you should be okay, and there should not be anything wrong with the coordinates in MiTranscriptome. 

-Yashar 

[pariche...@gmail.com]

Hi Dear Dr, Niknafs

My theses is based on MiTranscriptome database .  regarding that I am a beginner in this field I have some problems that may seem to be a little simple. One of them is finding annoatated lncRNAs in other databases by their miTranscriptome symbols and geneIDs. Would you please help me to know about this? I woulg really appreciated any help from you.

best rgards

Maleki,p

National Institute of Genetic Engineering and Biotechnology

Tehran,Iran

 

[Yashar Niknafs]

Will answer on your other thread. Thanks!

-Yashar 

[Yashar Niknafs]

Hello Leonie, 

So the emsembl annotaton of a gene is a curated structure for the gene. The MiTranscriptome is a collection of gene structure predictions from RNA-seq data. So it is almost expected that the two would differ at least slightly for most genes. Although HG19 is the genome used for both transcriptomes, the actual gene structures may differ from annotation to annotation. You'll note that for many genes refseq is not equal to GENCODE which is not equal to MiTranscriptome, etc. 

Does that make sense? 

-Yashar