Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: lncRNA gene vs. lncRNA isoform
0
gravatar for tungl
2.3 years ago by
tungl • 0
U.S.A.
tungl • 0 wrote:

If one of the gene isoforms (or one of the transcripts) is lncRNA, can we just claim that this gene is a lncRNA gene?

In GENCODE lncRNA GTF file, for each gene, there is always an entry (the first entry) which has the transcript_id equal to the gene_id. What does this entry represent?

I’d appreciate your advice.

Thank you very much in advance!
gencode transcripts isoforms lncrna rna-seq • 684 views
ADD COMMENT • link •
modified 2.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.3 years ago by tungl • 0
1
gravatar for Jennifer Hillman Jackson
2.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The GTF entry represents a single long non-coding transcript. In my opinion, it would be more precise to interpret this as an "lncRNA transcript" rather than an "IncRNA gene". This data file represents a particular class of transcripts - not complete gene bound annotation.

To learn more about how to interpret the content and the way the annotation is modeled, please review:

Others are welcome to comment further.

Best, Jen, Galaxy team
ADD COMMENT • link modified 2.3 years ago • written 2.3 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour