Table 1.
Statistics on the detected isoforms in the house mouse populations and outgroups
| M. m. domesticus | M. m. musculus | M. m. castaneus | M. spicilegus | M. spretus | |||
|---|---|---|---|---|---|---|---|
| GE (N: 8) | FR (N: 8) | IR (N: 8) | KA (N: 8) | TA (N: 8) | SL (N: 4) | SP (N: 4) | |
| Unique isoforms | 23,027 (SD:2001) | 21,609 (SD:2315) | 21,763 (SD:2006) | 22,380 (SD:1553) | 21,279 (SD:1532) | 20,644 (SD:858) | 21,640 (SD:640) |
| Protein-coding | 21,394 (SD:2062) | 20,024 (SD:2431) | 20,155 (SD:1941) | 20,798 (SD:1486) | 19,642 (SD:1435) | 18,786 (SD:929) | 20,063 (SD:597) |
| Nonsense-mediated decay (NMD) | 1152 (SD:226) | 1071 (SD: 220) | 1098 (SD:209) | 1125 (SD:146) | 1142 (SD:216) | 1038 (SD:146) | 1131 (SD:46) |
| Non-protein-coding | 1634 (SD:239) | 1585 (SD:284) | 1608 (SD:324) | 1582 (SD:235) | 1637 (SD:261) | 1858 (SD:73) | 1577 (SD:63) |
| Known isoforms | 17,266 (SD:1216) | 16,306 (SD: 1419) | 16,343 (SD:1257) | 16,487 (SD:861) | 15,765 (SD:821) | 15,202 (SD:512) | 15,608 (SD:416) |
| Full splice match (FSM) | 15,007 (SD:1217) | 14,245 (SD: 1441) | 13,654 (SD:1053) | 14,466 (SD:810) | 13,561 (SD:602) | 12,812 (SD:523) | 13,621 (SD:297) |
| Incomplete splice match (ISM) | 2259 (SD:297) | 2060 (SD: 654) | 2689 (SD:531) | 2021 (SD:593) | 2204 (SD:313) | 2389 (SD:325) | 1988 (SD:154) |
| Novel isoforms | 5762 (SD:796) | 5304 (SD: 913) | 5421 (SD:778) | 5893 (SD:708) | 5514 (SD:768) | 5442 (SD:415) | 6032 (SD:237) |
| Not in category (NIC) | 3765 (SD:599) | 3490(SD:651) | 3478 (SD:514) | 3611 (SD:459) | 3469 (SD:528) | 3204 (SD:318) | 3582 (SD:165) |
| Novel not in category (NNC) | 1811 (SD:202) | 1647 (SD: 271) | 1768 (SD:256) | 2066 (SD:254) | 1839 (SD:234) | 2015 (SD:120) | 2248 (SD:59) |
| Fusion (F) | 74 (SD:11) | 67 (SD:15) | 78 (SD:11) | 90 (SD:18) | 93(SD:17) | 65 (SD:7) | 84 (SD:8) |
| Genic (G) | 22 (SD:5) | 19 (SD:4) | 18 (SD:5) | 22 (SD:4) | 25 (SD:4) | 24 (SD:1) | 24 (SD:3) |
| Antisense (A) | 35 (SD:8) | 30 (SD:10) | 33 (SD:12) | 32 (SD:6) | 30 (SD:10) | 49 (SD:12) | 31 (SD:3) |
| Intergenic (I) | 54 (SD:7) | 51 (SD:13) | 44 (SD:14) | 72 (SD:10) | 59 (SD:15) | 84 (SD:6) | 62 (SD:10) |
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The digit succeeding the character N indicates the number of sequenced mouse individuals in each population. The graphic depiction of isoform categories is shown in Figure 4A. Isoforms categorized as FSM and ISM are defined to be known isoforms, gene loci with any isoform not categorized as either Antisense or Intergenic to be annotated genes. SD values refer to variances between the individuals in a given population.
