Can a gene only expresses as a lncRNA？
Is it possible that a gene is composed of exons without introns and only expresses as a lncRNA？
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Ram
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lewisbatmanarnold •
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lewisbatmanarnold •
2 answers
See A:
You can easily download gencode annotation and filter genes transcripts according the number of exons.
Clumsy but works:
curl -s "ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_21/gencode.v21.long_noncoding_RNAs.gtf.gz" |
gunzip -c |
awk '($3=="exon") {print $12}' |
sort | uniq -c |
awk '($1 == 1) {print $2}' | head -n 5
"ENST00000313031.2";
"ENST00000313737.5";
"ENST00000313865.6";
"ENST00000317726.4";
"ENST00000319817.3";
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In other words, "Are there any lncRNAs with only one exon?"
Some well known lincRNAs (such as MALAT1) are single exonic. So technically yes.