UBIQUITIN GENES IN DROSOPHILA MELANOGASTER
Steven Marygold, personal communication to FlyBase (12th January 2007)
    I used the sequence of the best (only?) characterised ubiquitin gene in Dmel (Ubi-p63E, FBgn0003943) to search for additional ubiquitin genes in the Dmel genome (annotated protein sequences) by BLASTp (using Ubi-p63E-PA, FBpp0073034 as the query).  I repeated these BLAST searches using a human ubiquitin sequence (ubiquitin C (UBC), NP_066289.2) as the query (obtaining essentially identical results) and a mouse ubiquitin sequence (ubiquitin B, NP_035794) as the query (obtaining similar results).  ie:
    With Dm Ubi-p63E or Hs ubiquitin C:
    Ubi-p63E (FBgn0003943), E = 0.0
    CG32744 (FBgn0052744), E = 0.0
    CG11700 (FBgn0029856), E = e-149 (4x UBI)
    RpL40 (FBgn0003941), E = 6e-37
    RpS27A (FBgn0003942), E = 2e-36
    With Mm ubiquitin B:
    Ubi-p63E (FBgn0003943), E = e-169
    CG32744 (FBgn0052744), E = e-169
    CG11700 (FBgn0029856), E = e-150
    RpL40 (FBgn0003941), E = 4e-37
    RpS27A (FBgn0003942), E = 5e-37
    (Note: The ribosomal proteins RpL40 and RpS27A appear in these lists because they each encode a fusion protein: ubiquitin forms the N-terminal half of the protein, while the ribosomal protein forms the C-terminal half.  (Once made, I believe that the fusion protein is cleaved into the two individual proteins.)
    Interestingly, CG32744 and CG11700 lie in bands 5E4 and 5E5, respectively, with only one other gene (CG32745) between the two of them.  Thus, CG32744 and CG11700 (together) almost certainly correspond to the previously uncloned 'Ubi-p5E' gene.
    Judging from EST counts, CG32744 is highly expressed, while CG11700 has no known ESTs associated with it.  However, there appears to be one cDNA (AY118459/GH17513) on GBrowse that links the CG32744 and CG11700 sequences into one transcript, suggesting that these two genes may in fact be a single gene with CG11700 acting as an infrequently used alternative first exon.
    If they are indeed two separate genes, then I propose that CG32744 be renamed Ubi-p5E4, and CG11700 be renamed Ubi-p5E5 (to be consistent with the current nomenclature); the gene record corresponding to 'Ubi-p5E' should then be deleted with the information stored under it added to both of these new genes.
    If CG32744 and CG11700 are in fact a single gene, then the CG32744, CG11700 and Ubi-p5E gene records will need to be merged.
 realname: Steven Marygold