Extended Data Table 2 |.
Summary of transcripts used for visualizing read density
| Figure | Gene name | GENCODE (vM23) | Genome coordinate (mm10) | Height on track* | Length (bp) | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene ID | Transcript ID | Chr | Start | End | Exon | 5’UTR | CDS | 3’UTR | |||
| Fig. 1b | Ctcf | ENSMUSG00000005698.15 | ENSMUST00000005841.15 | chr8 | 105636578 | 105682922 | 5276 | 3781 | 267 | 2208 | 1306 |
| Dnmt3a | ENSMUSG00000020661.15 | ENSMUST00000020991.14 | chr12 | 3807029 | 3914443 | 11420 | 9684 | 261 | 2724 | 6699 | |
| Usp2 | ENSMUSG00000032010.15 | ENSMUST00000065461.8 | chr14 | 44084938 | 44094477 | 2056 | 249 | 1188 | 619 | 2056 | |
| Klf4 | ENSMUSG00000003032.8 | ENSMUST00000107619.2 | chr4 | 55527142 | 55532466 | 12290 | 3028 | 594 | 1449 | 985 | |
| Fig. 2e | Zscan4b | ENSMUSG00000095339.2 | ENSMUST00000168158.2 | chr7 | 10900739 | 10905050 | 1583 | 1753 | 178 | 1515 | 60 |
| Cdx2 | ENSMUSG00000029646.3 | ENSMUST00000031650.3 | chr5 | 147300804 | 147307270 | 9397 | 2260 | 287 | 933 | 1040 | |
| Nanog | ENSMUSG00000012396.12 | ENSMUST00000012540.4 | chr6 | 122707567 | 122714633 | 8879 | 2210 | 214 | 915 | 1081 | |
| Pou5f1 | ENSMUSG00000024406.16 | ENSMUST00000025271.16 | chr17 | 35506017 | 35510772 | 12160 | 1361 | 81 | 1056 | 224 | |
| Tead4 | ENSMUSG00000030353.15 | ENSMUST00000112157.3 | chr6 | 128228180 | 128300813 | 11890 | 1908 | 568 | 1152 | 188 | |
| Sox2 | ENSMUSG00000074637.7 | ENSMUST00000099151.5 | chr3 | 34650404 | 34652461 | 10340 | 2056 | 10 | 957 | 1089 | |
| Gata6 | ENSMUSG00000005836.10 | ENSMUST00000047762.9 | chr18 | 11052469 | 11085635 | 12870 | 3233 | 310 | 1767 | 1156 | |
| Fig. 3b | Glce | ENSMUSG00000032252.14 | ENSMUST00000034785.7 | chr9 | 62057247 | 62070606 | 7822 | 4625 | 5 | 1854 | 2766 |
| Tbc1d8 | ENSMUSG00000003134.10 | ENSMUST00000054462.10 | chr1 | 39371491 | 39478755 | 5271 | 4450 | 188 | 3402 | 860 | |
| Gcnt4 | ENSMUSG00000091387.2 | ENSMUST00000171324.2 | chr13 | 96924688 | 96950906 | 6518 | 5086 | 377 | 1365 | 3344 | |
| Klf9 | ENSMUSG00000033863.2 | ENSMUST00000036884.2 | chr19 | 23141225 | 23168134 | 4703 | 4485 | 528 | 732 | 3225 | |
| Peg10 | ENSMUSG00000092035.8 | ENSMUST00000176551.2 | chr6 | 4747405 | 4760517 | 5999 | 6566 | 1474 | 1812 | 3280 | |
| Jadel | ENSMUSG00000025764.14 | ENSMUST00000026865.14 | chr3 | 41555730 | 41616864 | 5962 | 5480 | 114 | 2502 | 2864 | |
| Ube3a | ENSMUSG00000025326.12 | ENSMUST00000200758.3 | chr7 | 59228801 | 59311536 | 4789 | 9855 | 636 | 2610 | 6609 | |
| Extended Data Fig. 2 | Lrrcl 7 | ENSMUSG00000039883.5 | ENSMUST00000035651.5 | chr5 | 21543562 | 21575904 | 5961 | 2153 | 278 | 1329 | 546 |
| Cdh4 | ENSMUSG00000000305.12 | ENSMUST00000000314.12 | chr2 | 179442430 | 179899373 | 805 | 6387 | 190 | 2739 | 3458 | |
| Zfp52 | ENSMUSG00000051341.6 | ENSMUST00000233281.1 | chr17 | 21535538 | 21562601 | 910 | 3163 | 453 | 2172 | 538 | |
| Slc2a3 | ENSMUSG00000003153.10 | ENSMUST00000032476.10 | chr6 | 122727808 | 122742745 | 10830 | 3958 | 354 | 1479 | 2125 | |
| Actr5 | ENSMUSG00000037761.16 | ENSMUST00000045644.8 | chr2 | 158624887 | 158639211 | 1413 | 2401 | 253 | 1824 | 324 | |
| Klf5 | ENSMUSG00000005148.8 | ENSMUST00000005279.7 | chr14 | 99298690 | 99315036 | 35260 | 3351 | 303 | 1338 | 1710 | |
| Dhx37 | ENSMUSG00000029480.13 | ENSMUST00000169485.5 | chr5 | 125413857 | 125434121 | 1652 | 4759 | 83 | 3450 | 1226 | |
| Eomes | ENSMUSG00000032446.14 | ENSMUST00000035020.14 | chr9 | 118478343 | 118486132 | 16660 | 3559 | 315 | 2121 | 1123 | |
| Gata3 | ENSMUSG00000015619.10 | ENSMUST00000102976.3 | chr2 | 9857077 | 9878600 | 35620 | 3214 | 590 | 1329 | 1295 | |
| Klf4 | ENSMUSG00000003032.8 | ENSMUST00000107619.2 | chr4 | 55527142 | 55532466 | 12290 | 3028 | 594 | 1449 | 985 | |
| Myc | ENSMUSG00000022346.15 | ENSMUST00000160009.1 | chr15 | 61987421 | 61990253 | 3267 | 1764 | 99 | 1317 | 348 | |
| Yap1 | ENSMUSG00000053110.13 | ENSMUST00000086580.11 | chr9 | 7931998 | 8004588 | 7613 | 4114 | 197 | 1416 | 2501 | |
| Fgfr2 | ENSMUSG00000030849.18 | ENSMUST00000117872.7 | chr7 | 130162511 | 130266245 | 3778 | 4222 | 603 | 2169 | 1450 | |
*
The maximal value of read density plotted in the figures. The unit is RPKM.