Figure 4. Cis- or trans-spiced mtRNA in ESTs.

Alignment of the mt-part of EST BF306729 (BF3) with mtDNA (mt) and a corresponding NUMT on chromosome 5 (Chr 5) shows that the EST matches better to the mtDNA than to the NUMT, suggesting that the mt-sequence is more likely to be transcribed from mtDNA, but not its nuclear counterpart. Mismatched positions are often deletions. AV729737 is an mt-only EST that has an “AAAA” deletion when aligned with mtDNA. BE898652 is a trimera containing trans-spliced mt-sequence. Its 3–64th nt region is matched to the L-strand of an mtDNA (AC_000021), which is part of the ATP8 gene's antisense, while its 63–461st nt sequence is matched to the 8586–8986th nt of the L-strand, which is part of the ATP6 gene's antisense. The two sequences overlap at the boldfaced lowercase “tg”. The last part of this EST (underlined) is part of the PSMC4 mRNA from chromosome 19. AV702773 is a chimera. Its 1–245th nt region belongs to the last 3 exons of the PSME2 mRNA from chromosome 14, which is followed first by a poly-A signal (the 246–263rd nt, containing a T) and then by an mt-sequence (265–708th nt) from the 16S rRNA gene (the 2639–3082nd nt of mtDNA). However, since the PSME2 mRNA (NM_002818.2) in the NCBI database does not have a poly-A signal or a poly-A tail, it is unclear whether this poly-A is part of PSME2 that is undocumented or is part of the following mtRNA that is polyadenylated. Note that one long and two short italicized lowercase sequences in grey within the mtDNA region do not actually exist in, i.e. are deleted from, AV702773. Several single lowercase letters in grey are mismatches to the mtDNA (AY195786.2).