Mitochondrial Genome Annotation Difference?

Question

[Honey]

Following C: mitochondrial genome, I downloaded the annotation for mouse mitochondrial genome from http://uswest.ensembl.org/info/data/ftp/index.html and I found 13 genes as : EntrezGene ID Chromosome Name Transcript Start (bp) Transcript End (bp) Associated Gene Name MT 1 68 mt-Tf 17716 MT 2751 3707 mt-Nd1 17717 MT 3914 4951 mt-Nd2 17708 MT 5328 6872 mt-Co1 17709 MT 7013 7696 mt-Co2 17706 MT 7766 7969 mt-Atp8 17705 MT 7927 8607 mt-Atp6 17710 MT 8607 9390 mt-Co3 17718 MT 9459 9806 mt-Nd3 17720 MT 9877 10173 mt-Nd4l 17719 MT 10167 11544 mt-Nd4 17721 MT 11742 13565 mt-Nd5 17722 MT 13552 14070 mt-Nd6 17711 MT 14145 15288 mt-Cytb

However when I used - ENA repository @ http://www.ebi.ac.uk/ena/data/view/J01420 I found totally a different set of genes most of them are tRNA annotated.

How could that happen? AM I missing something. I need to use http://www.ebi.ac.uk/ena/data/view/J01420 to map my chipseq data and then I could not find bed file corresponding to this genome. Mouse mitochondrial genome should be well conserved. Thanks

Answer 1

[Bert Overduin]

The 13 protein-coding genes you found in Ensembl are represented in the CDS track on the ENA view you refer to.

The tRNA genes shown on the ENA view are present in the file ftp://ftp.ensembl.org/pub/release-72/fasta/mus_musculus/ncrna/Mus_musculus.GRCm38.72.ncrna.fa.gz.

So, no discrepancies between the two.