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Table 1 Gene annotations from which exon-exon junctions were extracted and unioned to obtain a list of annotated junctions

From: Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive

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]
  1. 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