Dear community,

I am working with a gene family across a wide range of chordate species, and one of the steps was to retrieve potential homologs from Ensembl. Interestingly, there were some of these genes that had their ID deprecated in newer versions of Ensembl. However, annotated sequences from these deprecated genes had reasonably good quality, and they matched the phylogenetic position that I'd expect, in phylogenetic analyses (so I could tentatively assume that the annotation was correct). 
I am curious of the reasons why some gene annotations are deprecated from version to version, even though they look like the annotation is correct, and whether it is wise to use such sequences nonetheless.

All best,
All these genes are slightly different.

The Mouse Lemur genes were all changed we moved to a new genome assembly. [ENSMICG00000011090](http://aug2017.archive.ensembl.org/Microcebus_murinus/Gene/Summary?db=core;g=ENSMICG00000011090;r=KQ056493.1:1017881-1023258;t=ENSMICT00000011083) and [ENSMICG00000011081](http://aug2017.archive.ensembl.org/Microcebus_murinus/Gene/Summary?g=ENSMICG00000011081;r=KQ056493.1:1033459-1039527) both disappeared when we moved from v2 to v3 of the assembly, whereas [ENSMICG00000011093](http://jul2016.archive.ensembl.org/Microcebus_murinus/Gene/Summary?db=core;g=ENSMICG00000011093;r=GeneScaffold_456:993434-999177;t=ENSMICT00000011088) was lost when we moved from v1 to v2. The good news is that the genes for two of them, [*HTR3C*](http://www.ensembl.org/Microcebus_murinus/Gene/Summary?db=core;g=ENSMICG00000049301;r=1:76618788-76624165;t=ENSMICT00000073294) and [*HTR3E*](http://www.ensembl.org/Microcebus_murinus/Gene/Summary?db=core;g=ENSMICG00000049068;r=1:76660281-76677598;t=ENSMICT00000072625) are in the latest version of Ensembl. The contigs underlying both of them have changed significantly, and this is the reason why the identifiers were changed and not mapped between the releases. I cannot find Mouse Lemur *HTR3D* in the current Ensembl database, although I suspect that [ENSMICG00000049384](http://www.ensembl.org/Microcebus_murinus/Gene/Summary?db=core;g=ENSMICG00000049384;r=1:76604424-76611926;t=ENSMICT00000072460) could be the correct gene based on sequence and genomic position – I will see if this ought to be annotated as this gene.

Kangaroo rat [ENSDORG00000003549](http://dec2016.archive.ensembl.org/Dipodomys_ordii/Gene/Summary?db=core;g=ENSDORG00000003549;r=GeneScaffold_6098:3429-11276;t=ENSDORT00000003549) is different. It was not lost when there was a new genome assembly. Looking that the gene on the assembly at that time, it has two exons that overlaps gaps in the assembly, which is probably why it was deprecated. Since it doesn't have a gene name, I [searched for the sequence using BLAST](http://www.ensembl.org/Dipodomys_ordii/Tools/Blast/Ticket?tl=NdAcgUH9C90qs6W6) in the current database, and there are few solid options for the gene it might be now. It has since had a new genome assembly and the gaps repaired, so could be annotated properly.