Gordon, more definitive answers will likely come from the annotation core
members, but here is what I understand
about this.  The mappings are completely dependent on NCBI content.

Working with

ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz

the header is

#Format: tax_id GeneID Symbol LocusTag Synonyms dbXrefs chromosome
map_location description type_of_gene Symbol_from_nomenclature_authority
Full_name_from_nomenclature_authority Nomenclature_status
Other_designations Modification_date (tab is used as a separator, pound
sign - start of a comment)

and, with some context, the record for 17710 is

> x[c(1,3516),]
     tax_id GeneID Symbol LocusTag             Synonyms
1     10090  11287    Pzp        - A1m|A2m|AI893533|MAM
3516  10090  17710   COX3        -                    -
                                                          dbXrefs chromosome
1    MGI:87854|Ensembl:ENSMUSG00000030359|Vega:OTTMUSG00000022212          6
3516                                                   MGI:102502         MT
           map_location                      description   type_of_gene
1    6 F1-G3|6 63.02 cM           pregnancy zone protein protein-coding
3516                  - cytochrome c oxidase subunit III protein-coding
     Symbol_from_nomenclature_authority
Full_name_from_nomenclature_authority
1                                   Pzp                  pregnancy zone
protein
3516                             mt-Co3 cytochrome c oxidase III,
mitochondrial
     Nomenclature_status
 Other_designations
1                      O alpha 1
macroglobulin|alpha-2-M|alpha-2-macroglobulin
3516                   O
  -
     Modification_date  X
1             20130804 NA
3516          20130804 NA

I would conjecture that the solution needs to come from NCBI -- they may
have neglected to deal properly with the MT genes in this case, as the
following computation suggests.  The symbols for which field "Symbol" does
not agree
with field "Symbol_from_nomenclature_authority" are

> xsn[xs!=xsn]
   [1] "mt-Atp6" "mt-Atp8" "mt-Co1"  "mt-Co2"  "mt-Co3"  "mt-Cytb" "mt-Nd1"
   [8] "mt-Nd2"  "mt-Nd3"  "mt-Nd4"  "mt-Nd4l" "mt-Nd5"  "mt-Nd6"  "mt-Rnr1"
  [15] "mt-Rnr2" "mt-Ta"   "mt-Tc"   "mt-Td"   "mt-Te"   "mt-Tf"   "mt-Tg"
  [22] "mt-Th"   "mt-Ti"   "mt-Tk"   "mt-Tl1"  "mt-Tl2"  "mt-Tm"   "mt-Tn"
  [29] "mt-Tp"   "mt-Tq"   "mt-Tr"   "mt-Ts1"  "mt-Ts2"  "mt-Tt"   "mt-Tv"
  [36] "mt-Tw"   "mt-Ty"


On Fri, Aug 9, 2013 at 11:17 PM, Gordon K Smyth <smyth@wehi.edu.au> wrote:

> Dear Biocore,
>
> We make a strong effort to use current NCBI official gene symbols and
> names in all our work, and we make much use of the excellent Bioconductor
> packages org.Mm.eg.db and org.Hs.eg.db for this purpose.
>
> I have recently noticed that org.Mm.eg.db is giving incorrect official
> names for mitochondrial genes.  It is giving human symbols for these genes
> instead of mouse symbols.  For example
>
>   > mappedRkeys(org.Mm.egSYMBOL["**17710"])
>   [1] "COX3"
>
> According to both Entrez Gene
>
>   http://www.ncbi.nlm.nih.gov/**gene/?term=17710<http://www.ncbi.nlm.nih.gov/gene/?term=17710>
>
> and MGI
>
>   http://www.informatics.jax.**org/marker/MGI:102502<http://www.informatics.jax.org/marker/MGI:102502>
>
> the official symbol is "mt-Co3".  This has been the official symbol for at
> least 4 years and probably longer.
>
> The correct name is not even included as an Alias:
>
>   > mappedRkeys(revmap(org.Mm.**egALIAS2EG)["17710"])
>   [1] "COX3"
>
> COX3 is the actually the symbol for the human ortholog.  It should only be
> an alias for the mouse gene.
>
> Same for all the mitochondrial genes.  In all cases, org.Mm.egSYMBOL is
> giving the human symbol instead of the mouse symbol.
>
> Is this deliberate?  If not, can you please fix?
>
> Thanks a lot
> Gordon
>
> ------------------------------**---------------
> Professor Gordon K Smyth,
> Bioinformatics Division,
> Walter and Eliza Hall Institute of Medical Research,
> 1G Royal Parade, Parkville, Vic 3052, Australia.
> http://www.statsci.org/smyth
>
>
>  sessionInfo()
>>
> R version 3.0.1 Patched (2013-07-04 r63183)
> Platform: i386-w64-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_Australia.**1252
> [2] LC_CTYPE=English_Australia.**1252
> [3] LC_MONETARY=English_Australia.**1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets
> [7] methods   base
>
> other attached packages:
> [1] org.Mm.eg.db_2.9.0   org.Hs.eg.db_2.9.0   RSQLite_0.11.4
> [4] DBI_0.2-7            AnnotationDbi_1.22.6 Biobase_2.20.0
> [7] BiocGenerics_0.6.0   limma_3.17.20
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.18.2 stats4_3.0.1
>
>
> ______________________________**______________________________**__________
> The information in this email is confidential and inte...{{dropped:13}}

