Table 1.
Gene annotations from which exon-exon junctions were extracted and unioned to obtain a list of annotated junctions
| Gene annotation | Number of junctions | Reference |
|---|---|---|
| hg19 | ||
| AceView | 395,410 | [12] |
| CCDS | 174,337 | [43] |
| GENCODE v19 | 343,887 | [2] |
| UCSC | 264,339 | [10] |
| lincRNAs | 30,256 | [6] |
| MGC | 160,388 | [44] |
| RefSeq | 235,512 | [1] |
| SIB | 414,422 | [45] |
| Vega | 242,672 | [2] |
| hg38 | ||
| CCDS | 178,775 | [43] |
| GENCODE v24 | 346,547 | [2] |
| UCSC | 356,644 | [10] |
| lincRNAs | 29,940 | [6] |
| MGC | 169,302 | [44] |
| RefSeq | 247,577 | [1] |
| SIB | 433,606 | [45] |
All tracks were taken from the UCSC Genome Browser [10] except for GENCODE [2], which was downloaded from the GENCODE website http://www.gencodegenes.org/releases/. Junction coordinates from hg38 annotations were lifted over to hg19 before the union was performed. Of all gene annotations listed here, the Swiss Institute of Bioinformatics (SIB) genes has the most, with more than 400,000 junctions for each of hg19 and hg38