GenBank conflicting annotations (identical proteins with different exons)

Question

[Eli Korvigo]

Here is the RefSeq mitochondrial complete genome record of Daucus carota

DEFINITION  Daucus carota subsp. sativus mitochondrion, complete genome.
ACCESSION   NC_017855
VERSION     NC_017855.1  GI:386799229
DBLINK      BioProject: PRJNA162951

It lists 2 identical proteins (NADH dehydrogenase subunit 5):

CDS         complement(join(220476..220625,221826..222220,
            51521..51542,33278..34495,35349..35576))
            /gene="nad5"
            /locus_tag="DacassM_p009"
            /trans_splicing
            /codon_start=1
            /product="NADH dehydrogenase subunit 5"
            /protein_id="YP_006291783.1"

CDS         complement(join(267858..268007,269208..269602,
            51521..51542,33278..34495,35349..35576))
            /gene="nad5"
            /locus_tag="DacassM_p008"
            /trans_splicing
            /codon_start=1
            /product="NADH dehydrogenase subunit 5"
            /protein_id="YP_006291784.1"

The proteins are 100% identical, though exons are different. It doesn't seem right to me. How is this possible?

Answer 1

[Markus]

If you look into the gene anntotation you see that the first one is also annotated as 'copy 2'. Repeats are very common in plant mitochondrial genomes, maybe you should have a look into the respective paper at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413510/.