Table 5.
Effects of the variation between homologous transcript sequences of the NOD and C57BL/6J Idd regions on the GRCm38 reference genome annotation
| Variation effect | All transcripts | Canonical transcripts |
|---|---|---|
| CODON_CHANGE_PLUS_CODON_DELETION | 8 | 2 |
| CODON_CHANGE_PLUS_CODON_INSERTION | 2 | 2 |
| CODON_DELETION | 6 | 3 |
| CODON_INSERTION | 10 | 5 |
| EXON | 2142 | 0 |
| FRAME_SHIFT | 7 | 3 |
| INTRON | 189 366 | 61 717 |
| NON_SYNONYMOUS_CODING | 640 | 326 |
| SPLICE_SITE_ACCEPTOR | 3 | 0 |
| SPLICE_SITE_DONOR | 12 | 6 |
| START_GAINED | 68 | 17 |
| STOP_GAINED | 1 | 1 |
| STOP_LOST | 1 | 0 |
| SYNONYMOUS_CODING | 1428 | 723 |
| SYNONYMOUS_STOP | 4 | 3 |
| UTR_3_PRIME | 2372 | 1192 |
| UTR_5_PRIME | 571 | 230 |
| WITHIN_NON_CODING_GENE | 736 | 609 |
| WITHIN_PSEUDOGENE | 660 | 636 |
The account of effects varies as all homologous transcripts in a gene or only the canonical transcript (the one with longest CDS or the longest length) are considered. EXON, WITHIN_NON_CODING_GENE and WITHIN_PSEUDOGENE refer to variants affecting exons of non-coding transcripts in coding genes, lncRNA genes and pseudogenes, respectively.