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Multiple reasons for that: since cdot 0.2.26, it contains fake-rna-* transcripts for MT transcripts that refseq does not have. However, not all of the refseq cdot data release files actually contain that information.
Also, because these are synthetic entries, the corresponding sequence may be missing from the seqrepo we use during building of the txdb -- which is why I re-enabled grafting the MT txs from ensembl onto refseq again (not yet pushed).
Describe the bug
Currently, mehari does not annotate tx on the MT chromosome.
Interestingly the information for the gene is available via annonars:
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