Table 1.
Identified Usher syndrome–associated retinal transcript isoforms and prevalent events observed across the majority of transcripts
| Gene | Clinical subtype | Identified retinal transcript isoforms | Corresponding figures | |
|---|---|---|---|---|
| Identified Ensembl Spliced Transcripts (ENST) | Validated novel events and previously unidentified transcriptsc | |||
| MYO7A | USH1B | ENST00000409709.9 (MANE) | Alternative transcription start site (transcript20055.Chr11.nic) | Figure 3 |
| ENST00000458637.6 | ||||
| USH1C | USH1C | ENST00000527020.5 | Supplemental Figure S1 | |
| ENST00000318024.9 | ||||
| ENST00000526313.5 | ||||
| CDH23 | USH1D | ENST00000224721.12a | Supplemental Figure S2 | |
| ENST00000461841.7 | Novel in frame exon 11A and skipping of micro exon 12 (transcript11235.Chr10.nnic) | |||
| ENST00000475158.1 | Exon 69 skipping | |||
| PCDH15 | USH1F | ENST00000644397.2 (MANE) | Supplemental Figure S3 | |
| ENST00000373957.7 | ||||
| ENST00000621708.4 | ||||
| ENST00000373955.5 | ||||
| SANS | USH1G | ENST00000614341.5 (MANE) | Supplemental Figure S4 | |
| CIB2 | USH1Jd | – | Supplemental Figure S5 | |
| USH2A | USH2A | ENST00000307340.8 (MANE)b | 5′ UTR splice events (transcript51429.Chr1.nnic; transcript51430.Chr1.nnic; transcript51439.Chr1.nnic) | Figure 5 |
| ENST00000366942.3 | ||||
| ADGRV1 | USH2C | ENST00000638316.1 | Figure 6 and Supplemental Figure S6 | |
| ENST00000639884.1 | ||||
| ENST00000640109. | ||||
| ENST00000640281.1 | ||||
| WHRN | USH2D | ENST00000362057.4 (MANE) | Inclusion of novel exon 7B (transcript13724.Chr9.nnic) |
Figure 4 |
| ENST00000374057.3 | Intron 4 retention (transcript13718.Chr9.nnic) | |||
| ENST00000265134.10 | ||||
| CLRN1 | USH3A | ENST00000327047.6 (MANE) | Supplemental Figure S7 | |
| ENST00000472224.1 | ||||
| ARSG | USH4 | ENST00000448504.6 | Supplemental Figure S8 | |
| ENST00000578726.1 | ||||
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aPresence of transcript isoform is based solely on manual curation of sequenced reads of the sample prepared following the optimized PacBio long transcript workflow.
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bPresence of transcript isoform is based solely on results of Samplix Xdrop targeted enrichment.
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cEvents are validated using raw sequencing reads of an ONT long-read sequencing data set of independent retina samples.
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dThe association of CIB2 with USH1J has been called into question (Booth et al. 2018).
