Figure 7. ψmRNA Examples.

(A) Ubiquitin-conjugating enzyme E2D pseudogene and ψmRNAs on mouse Chromosome 11. Protein homologies (blue track at top) of human UBE2D and mouse Ube2 paralogues to mouse genomic sequence indicate an unprocessed pseudogene (two frameshifts, see alignment panels, blue gene object). Mouse FANTOM mRNAs (brown tracks, with accession numbers) match genomic sequence without disruption (see alignment panels). No current mouse cDNAs or ESTs support the precise exon structure equivalent to the expressed human UBE2D gene: for example exon three (indicated) is larger than in the human orthologue. FANTOM mRNAs support two splice variants (red gene objects, numbers two and three from top). Two remaining splice variants are based on mouse EST matches (not shown). Pictures are from AceDB F-map (top) and Blixem (alignments, bottom), modified for clarity.

(B) Compensatory frameshifts in FANTOM clone E030045F20 (AK053223) (brown track on the right) on mouse Chromosome 11, caused by splice variation in a gene homologous to human C22 orf3 at both the 5′ and 3′ end of an internal exon on mouse Chromosome 11. The more common variant is represented by FANTOM mRNA AK077457. The two transcripts (green gene objects on the left) have a different translation for the top exon shown here (blue and red highlights on the translations, for the objects marked with blue and red dots, respectively). Outlines on the DNA sequence show the respective exon boundaries and splice sites. The second exon shown is translated in the same reading frame for both variants (purple highlight), as are preceding and further downstream exons (not shown). A third variant, FANTOM mRNA BC062155, is a non-translating ψmRNA, as it has an out-of-frame alternative splice acceptor but lacks a compensating out-of-frame alternative splice donor site (red gene object on the left). Pictures are from AceDB F-map, modified for clarity.