[ensembl-dev] 100% identical genes

[Podtelezhnikov, Alexei]

Public

Dear Ensembl team,

Here is probably incomplete list of 100% identical sequences in Rnor_6.0.

Cyp2b1 RGD:2466   and   LOC108348266 RGD:11439359
Cyp3a23-3a1 RGD:628626   and    LOC100910877 RGD:6495986
A2m RGD:2004   and   LOC100911545 RGD:6492449 
LOC100360087 RGD:2322860   and   Ftl1 RGD:61813
LOC102549542 RGD:7527008   and   Elovl6 RGD:620585

Such genes present a problem to RNA-Seq aligners and might result in wrong quantification. I noticed that Ensembl removed some but not all duplicated genes. Do you keep a full list of such genes? Would you consider them genome assembly errors and, therefore, flag, fix, or remove them?

Thank you,
Alexei
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