Projection rates of mouse RefSeq and GenBank mRNA transcripts and exons on the rat genome
|
|
Mouse exons |
Pct. (%) |
Mouse transcripts |
Pct. (%) |
|---|---|---|---|---|
| Original | NA | NA | 125,972 | NA |
| Aligned on mouse | 761,241 | 100 | 119,280 | 100 |
| Projection stage | ||||
| Complete projections | 659,360 | 86.6 | 68,805 | 57.7 |
| Partial projections | 38,612 | 5.1 | 38,666 | 32.4 |
| Not projected | 64,062 | 8.4 | 11,809 | 9.9 |
| in unprojected transcripts | 38,991 | 5.1 | ||
| in projected transcripts | 25,071 | 3.3 | ||
| Total from complete and partial projections | 697,972 | 91.7 | 107,471 | 90.1 |
| Refinement stage | ||||
| Endorsed unaltered | 659,436 | 86.6 | 85,418 | 71.6 |
| canonical | 645,147 | 84.7 | ||
| non-canonical | 14,289 | 1.9 | ||
| Endorsed altered | 23,603 | 3.1 | 17,548 | 14.7 |
| by 1–10 bp | 19,145 | 2.5 | ||
| by >10 bp | 4,458 | 0.6 | ||
| Projected, not endorsed | 14,933 | 2.0 | 4,505 | 3.8 |
| Rejecteda | 40,004 | 5.3 | 4,505 | 3.8 |
| in rejected transcripts | 6,699 | 0.9 | ||
| in endorsed transcripts | 33,305 | 4.4 | ||
| Missedb (found with BLASTN) | 12,275 | 1.6 | NA | NA |
| Total endorsed projections
|
683,039
|
89.7
|
102,966
|
86.3
|
-
NA = not applicable.
For the projection stage, “complete” exon projections are defined as having both ends of the exon contained in matches; the exon projection is then the entire interval between the projected endpoints. “Complete” transcript projections have all exons “complete”; “partial” transcripts have at least one complete or partially projected exon. “Complete” and “partial” transcripts were submitted for refinement in stage two. For the refinement stage, endorsed unaltered “canonical” projections had canonical splice signals and did not necessitate alteration, whereas “non-canonical” ones failed extension to a nearby consensus splice site. “Missed” projections were based on the BLASTN search (E = 2.0, default parameters) of all rejected exons from endorsed transcripts against the genomic interval between their adjacent exons, for internal rejected exons, or a 50,000-bp interval past the aligned end of the transcript, for marginal rejected exons, consistently with the orientation of the transcript. A threshold of 50% length or minimum 50-bp coverage of the exon was applied to the BLASTN results.
-
↵a Includes the number of unprojected exons from partially projected transcripts
-
↵b Counted from the number of rejected exons from endorsed transcripts
