Linc and miRNA in GTF file

Question

[Sandeep]

While annotating the small RNA data using GTF file, we come across a few entries that have the gene name of miRNA, but the type of gene is lincRNA. Can anyone clarify this please?

Also, I extracted the region in question from the GTF file. I have pasted it below.

chr5    HAVANA  gene    148809849       148812397       .       +       .       gene_id "ENSG00000269936.2"; transcript_id "ENSG00000269936.2"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "MIR145"; transcript_type "lincRNA"; transcript_status "NOVEL"; transcript_name "MIR145"; level 2; havana_gene "OTTHUMG00000184101.1";
chr5    HAVANA  transcript      148809849       148812397       .       +       .       gene_id "ENSG00000269936.2"; transcript_id "ENST00000602315.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "MIR145"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "MIR145-001"; level 2; havana_gene "OTTHUMG00000184101.1"; havana_transcript "OTTHUMT00000468029.1";
chr5    HAVANA  exon    148809849       148812397       .       +       .       gene_id "ENSG00000269936.2"; transcript_id "ENST00000602315.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "MIR145"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "MIR145-001"; exon_number 1;  exon_id "ENSE00003379897.1";  level 2; havana_gene "OTTHUMG00000184101.1"; havana_transcript "OTTHUMT00000468029.1";
chr5    ENSEMBL transcript      148810209       148810296       .       +       .       gene_id "ENSG00000269936.2"; transcript_id "ENST00000384967.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "MIR145"; transcript_type "miRNA"; transcript_status "KNOWN"; transcript_name "MIR145-201"; level 3; tag "basic"; havana_gene "OTTHUMG00000184101.1";
chr5    ENSEMBL exon    148810209       148810296       .       +       .       gene_id "ENSG00000269936.2"; transcript_id "ENST00000384967.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "MIR145"; transcript_type "miRNA"; transcript_status "KNOWN"; transcript_name "MIR145-201"; exon_number 1;  exon_id "ENSE00001499974.1";  level 3; tag "basic"; havana_gene "OTTHUMG00000184101.1";

As we can see, all the lines of gtf file have gene_type "lincRNA" and gene_name "MIR145".

Also checked by entering the coordinates in UCSC, there is nothing visible when lincRNA track is enabled, but we can see mir145 when sno/miRNA track is enabled.

Basically, while we count the gene features using HTSeq, MIR145 is reported as linkRNA and it counts it as linkRNA instead of miRNA.

Do we consider it as linkRNA or miRNA?

Answer 1

[PoGibas]

Gene ENSG00000269936 is a long non-coding RNA that has 2 transcripts (~2kb and 90bp). I imagine that it might be a lncRNA that also codes a miRNA. Probably that's why its called "MIR*". And UCSC browser show this very clearly (GENCODE Genes V17 track).

[Sandeep]

Thats precisely the reason I posted this question. Because when we count using HTSeq and gencode v19 gtf file, we get mir145 as lincRNA. This is becuase in gtf file the gene type is lincRNA. So, I am wondering, if it is infact a lincRNA or miRNA!!!!

[mark.ziemann]

From what I understand the gene is classified as a lincRNA (has a long primary transcript seq), but the transcript is a miR as well as the long precursor.