What are these AGAPxxx identifiers and where are the old ENSANGxxx IDs?

Answer: 

The annotation of the Anopheles gambiae genome has been undertaken by a number of groups since the PEST publication in 2002. Currently, VectorBase provides Apollo to all members of the community that would like to contribute with manual annotations. VectorBase assumed responsibility for integrating the users manual annotations submited via Apollo to the official gene set. VectorBase decided to move away from the Ensembl stable identifier nomenclature in favor of a more FlyBase style system. In line with this the identifiers for Anopheles were changed to the VectorBase gene identifiers from genebuild 4. All VectorBase identifiers for An. gambiae begin with the 4 letters AGAP. The same numeric value is used for a gene and all its products (transcripts and proteins). Alternate products of a single gene have suffixes ending A, B, C etc.

Links

Convert Anopheles gambiae IDs

Go to A. gambiae Genome Browser front page and click on 'Update your old Ensembl IDs'

More details can be found about the AgamP3.4 gene build and there is also further practical guidance for conversion between identifiers available.