Extended Data Table 1 |.
The genomic locations of candidate LMI070-induced exons and the frequency of events from RNA-seq datasets
| GRCh38 | GRCh37 (hg19) | |||||||
|---|---|---|---|---|---|---|---|---|
| Gene ID | Genomic Minigene region | Pseudo exon position | DMSO Observed Avg Counts (J1, J2) | LMI070 Observed Avg Counts (J1, J2) | Genomic Minigene region | Pseudo exon position | LMI070 Binding sequence | |
| Exclusive | SF3B3 | chr16:70,526,657–70,529,199 | chr16:70,527,376–70,527,429 | 0, 0 | 31, 30.5 | chr16:70560560–70563102 | chr16:70561279–70561332 | AGAGTAAGAC |
| BENC1 | chr17:42,810,759–42,811,797 | chr17:42,811,292–42,811,330 | 0, 0 | 24.45, 15.75 | chr17:40962777–40963815 | chr17:40963310–40963348 | AGAGTAAGGC | |
| GXYLT1 | chr12:42,087,786–42,097,614 | chr12:42,095,151–42,095,214 | 0, 0 | 10.75, 23.75 | chr12:42481588–42491416 | chr12:42488953–42489016 | AGAGTATAGT | |
| SKP1 | chr5:134,173,809–134,177,053 | chr5:134,175,284–134,175,385 | 0, 0 | 5.75, 23.75 | chr5:133509500–133512744 | chr5:133510975–133511076 | AGAGTAGGAT | |
| SKP1 | chr5:134,173,809–134,177,053 | chr5:134,175,284–134,175,423 | 0, 0 | 15.25,11.75 | chr5:133509500–133512744 | chr5:133510975–133511114 | AGAGTAGGAT | |
| C12orf4 | chr12:4,536,017–4,538,508 | chr12:4,537,380–4,537,514 | 0, 0 | 17.5, 19 | chr12:4645183–4647674 | chr12:4646546–4646680 | AGAGTAAGAA | |
| SSBP1 | chr7:141,739,167–141,742,229 | chr7:141,741,310–141,741,459 | 0, 0 | 17.25, 2.25 | chr7:141438967–141442029 | chr7:141441110–141441259 | AGAGTAAGGC | |
| RARS | chr5:168,517,815–168,519,190 | chr5:168,518,369–168,518,523 | 0, 0 | 13.5, 1.5 | chr5:167944820–167946195 | chr5:167945374–167945528 | AGAGTAGGAT | |
| RARS | chr5:168,517,815–168,519,190 | chr5:168,518,469–168,518,523 | 0, 0 | 13.6, 1.75 | chr5:167944820–167946195 | chr5:167945474–167945528 | AGAGTAGGAT | |
| PDXDC2P | chr16:70,030,988–70,031,968 | chr16:70,031,186–70,031,248 | 0, 0 | 13.25, 10.25 | chr16:70064891–70065871 | chr16:70065089–70065151 | AGAGTAAGAA | |
| STRADB | chr2:201,469,953–201,473,076 | chr2:201,470,907–201,471,111 | 0, 0 | 9.5, 5.25 | chr2:202334676–202337799 | chr2:202335630–202335834 | AGAGTAAGGA | |
| WNK1 | chr12:894,562–896,732 | chr12:895,161–895,196 | 0, 0 | 9, 5.5 | chr12:1003728–1005898 | chr12:1004327–1004362 | AGAGTAGGTG | |
| WDR27 | chr6:169,660,663–169,662,424 | chr6:169,661,703–169,661,750 | 0, 0 | 8.5, 7.25 | chr6:170060759–170062520 | chr6:170061799–170061846 | AGAGTAAGCA | |
| CIP2A | chr3:108,565,355–108,566,638 | chr3:108,565,898–108,565,931 | 0, 0 | 7.75, 5 | chr3:108284202–108285485 | chr3:108284745–108284778 | AGAGTAAGAA | |
| ITF57 | chr3:108,191,521–108,206,696 | chr3:108,192,476–108,192,526 | 0, 0 | 7.25, 5.25 | chr3:107910368–107925543 | chr3:107911323–107911373 | AGAGTAGGCC | |
| HTT | chr4:3,212,555–3,214,145 | chr4:3213622–3213736 | 0, 0 | 7, 2.25 | chr4:3214282–3215872 | chr4:3215349–3215463 | AGAGTAAGGG | |
| SKA2 | chr17:59,112,228–59,119,514 | chr17:59119395–59119495 | 0, 0 | 6.75, 1 | chr17:57189589–57196875 | chr17:57196756–57196856 | AGAGTAAGAG | |
| EVC | chr4:5,733,318–5,741,822 | chr4:5741334–5741441 | 0, 0 | 6.5, 3 | chr4:5735045–5743549 | chr4:5743061–5743168 | AGAGTAAGCA | |
| DYRK1A | chr21:37,420,144–37,473,056 | chr21:37422581–37422652 | 0, 0 | 6.25, 6 | chr21:38792446–38845358 | chr21:38794883–38794954 | AGAGTAGGTT | |
| GNAQ | chr9:77,814,652–77,923,557 | chr9:77920648–77920703 | 0, 0 | 6, 1 | chr9:80429568–80538473 | chr9:80535564–80535619 | AGAGTAAGCT | |
| ZMYM6 | chr1:35,019,257–35,020,472 | chr1:35020261–35020279 | 0, 0 | 5.75, 4 | chr1:35484858–35486073 | chr1:35485862–35485880 | ACTGTGAGTA | |
| CYB5B | chr16:69,448,031–69,459,260 | chr16:69448605–69448753 | 0, 0 | 5.75, 1.25 | chr16:69481934–69493163 | chr16:69482508–69482656 | TAGGTGGTTC | |
| MMS22L | chr6:97,186,342–97,229,533 | chr6:97201362–97201465 | 0, 0 | 5.75, 2 | chr6:97634218–97677409 | chr6:97649238–97649341 | GAGGTGATTG | |
| MEMO1 | chr2:31,883,262–31,892,301 | chr2:31,887,035–31887087 | 0, 0 | 5, 2.25 | chr2:32108331–32117370 | chr2:32112104–32112156 | AGAGTAAGGT | |
| PNISR | chr6:99,416,278–99,425,413 | chr6:99420523–99420584 | 0, 0 | 5, 4 | chr6:99864154–99873289 | chr6:99868399–99868460 | AGAGTAGTGT | |
| Enriched | CACNA2D1 | chr7:82,066,406–82,084,958 | chr7:82,076,016–82,076,122 | 0.25, 0.75 | 18.5, 1.5 | chr7:81695722–81714274 | chr7:81705332–81705438 | CAGGTTGGTA |
| SSBP1 | chr7:141,739,083–141,742,248 | chr7:141741310–141741459 | 0.25, 0 | 16.75, 2.25 | chr7:141438883–141442048 | chr7:141441110–141441259 | AGAGTAAGGC | |
| DDX42 | chr17:63,805,048–63,806,672 | chr17:63,806,151–63,805,994 | 0.25, 0 | 13.75, 4.5 | chr17:61882408–61884032 | Unable to lift over | AGAGTAAGAT | |
| ASAP1 | chr8:130,159,817–130,167,688 | chr8:130,160,785–130,160,793 | 0.25, 0.25 | 13, 11.5 | chr8:131172063–131179934 | chr8:131173031–131173039 | AGAGTAAGTA | |
| DUXAP10 | chr14:19,294,564–19,307,199 | chr14:19,305,354–19,305,469 | 0.25, 0.75 | 9.5, 1.25 | chr14:19882243–19894878 | chr14:19893035–19893150 | AGAGTAAGGT | |
| AVL9 | chr7:32,558,783–32,570,372 | chr7:32,562,558–32,562,913 | 0.25, 0.5 | 7.5, 1.5 | chr7:32598395–32609984 | chr7:32602170–32602525 | AGAGTAAGAC | |
| DYRK1A | chr21:37,419,920–37,472,960 | chr21:37,422,582–37,422,652 | 0.25, 0 | 6.25, 6 | chr21:38792222–38845262 | chr21:38794884–38794954 | AGAGTAGGTT | |
| FAM3A | chrX:154,512,311–154,512,939 | chrX:154,512,568–154,512,706 | 0.25, 0 | 5.75, 1 | chrX:153740635–153741263 | chrX:153740892–153741030 | GGGGTAGGGA | |
| FHOD3 | chr18:36,740,620–36,742,886 | chr18:36,742,377–36,742,468 | 0.5, 0.25 | 15.25, 3.5 | chr18:34320583–34322849 | chr18:34322340–34322431 | AGAGTAAGAG | |
| TBCA* | chr5:77,707,994–77,777,000 | chr5:77,774,217 | 0.5 | 14 | chr5:77003819–77072824 | chr5:77070041 | ND | |
| MZT1 | chr13:72,718,939–72,727,611 | chr13:72,725,642–72,725,778 | 0.5, 1 | 13.25, 1.25 | chr13:73293077–73301749 | chr13:73299780–73299916 | AGAGTAAGAA | |
| LINC01296 | chr14:19,092,877–19,096,652 | chr14:19094556–19094671 | 0.5, | 8.25, | chr14:19680556–19684333 | chr14:19682237–19682352 | AGAGTAAGAT | |
| SF3B3 | chr16:70,541,627–70,544,553 | chr16:70544169–70544249 | 0.5, 0 | 8.25, 3 | chr16:70575530–70578456 | chr16:70578072–70578152 | AGAGTAAAGA | |
| SAFB | chr19:5,654,060–5,654,457 | chr19:5,654,140–5,654,368 | 0.5, 0 | 6.25, 2 | chr19:5654071–5654468 | chr19:5654151–5654379 | AGAGTAAGGA | |
| GCFC2 | chr2:75,702,163–75,706,652 | chr2:75,702,691–75,702,807 | 0.5, 0 | 6.25, 2 | chr2:75929289–75933778 | chr2:75929817–75929933 | TGAGTAAGAG | |
| MRPL45 | chr17:38,306,450–38,319,088 | chr17:38,312,587–38,312,661 | 0.5, 0 | 5.75, 1.25 | chr17:36462417–36474972 | chr17:36468550–36468624 | AGAGTAAGAC | |
| SPIDR | chr8:47,260,788–47,280,196 | chr8:47,273,337–47,273,450 | 0.5, 0 | 5.5, 1.75 | chr8:48173380–48192784 | chr8:48185929–48186042 | AGAGTAAGAC | |
| DUXAP8 | chr22:15,815,315–15,828,713 | chr22:15,817,119–15,817,234 | 0.75, 0.25 | 13.75, 1.25 | chr14:19,680,685–19,691,354 | chr14:19682237–19682352 | AGAGTAAGAT | |
| PDXDC1 | chr16:15,008,772–15,009,763 | chr16:15,009,499–15,009,561 | 2, 1 | 16.75, 1.5 | chr16:15102629–15103620 | chr16:15103356–15103418 | AGAGTAAGAA | |
| MAN1A2 | chr1:117,442,104–117,461,030 | chr1:117,456,085–117,456,206 | 0.75, 1 | 8, 5.25 | chr1:117984726–118003652 | chr1:117998707–117998828 | AGAGTAAGGT | |
| RAF1 | chr3:12,600,376–12,604,350 | chr3:12,603,478–12,603,537 | 1, 0.25 | 16.5, 1 | chr3:12641875–12645849 | chr3:12644977–12645036 | AGAGTAGGTA | |
| ERGIC3 | chr20:35,548,787–35,554,452 | chr20:35,549,163–35,549,207 | 1,0 | 7.5, 2.5 | chr20:34136540–34142223 | chr20:34136917–34136961 | GTGGTAGGTA | |
Summarized in this table are the differentially expressed candidate LMI070-induced splicing positions as identified by RNA-seq of HEK293 cells treated with either DMSO or LMI070 (25 nM). All candidates shown were manually selected from a bioinformatically generated list of top hits on the basis of their suitability for construction of an exon switching genomic minigene, their exclusivity to the LMI070 condition, and their minimal to undetectable levels in DMSO-treated cells. The top 25 rows (shaded green) indicate hits observed exclusively upon LMI070 exposure. The following 22 rows (shaded yellow) indicate candidates for which splicing was enriched but not totally exclusive to LMI070 treatment. Columns (from left to right) indicate: 1. Exclusivity to LMI070 induction. 2. The gene ID containing the splicing events of interest. 3. The GRCh38 genomic positions used to create the splice event-containing genomic minigene. 4. The GRCh38 genomic positions of the pseudo exon created by LMI070-induced splicing. 5. The average number of exon–exon junction spanning reads observed with DMSO treatment. 6. The average number of exon–exon junctions spanning reads observed with LMI070 treatment. To assess the frequency with which LMI070-induced events occur we queried Intropolis38, a database containing the frequency of splicing events observed across 21,504 human RNA-seq samples, representing a diverse set of human tissues and conditions. The reference genome used for the Intropolis database is GRCh37 so the LiftOver feature from the UCSC genome browser was used to convert the GRCh38 coordinates to GRCh37. 7. The GRCh37 genomic position of the minigene. 8. The GRCh37 genomic position of the pseudo exon. 9. The DNA sequence of the LMI070 binding sequence in the pseudo exon.