Table 3 Junction annotation sources. Descriptions are from the UCSC Table Browser track detail page or the Gencode website. See also Reference files
From: recount3: summaries and queries for large-scale RNA-seq expression and splicing
Short name | Description | Reference build |
|---|---|---|
Acembly | AceView gene models from cDNA by Danielle and Jean Thierry-Mieg at NCBI, using their AceView program | hg19, mm9 |
Chess 2.2 | Chess transcripts assembled using StringTie based on GTEx [44] | hg38 |
ccdsGene | Human genome high-confidence gene annotations from the Consensus Coding Sequence (CCDS) project | hg19, hg38, mm9, mm10 |
Gencode | 19 (hg19), 24-26, 29, 33 (hg38) 1 (mm9), 2-24 (mm10) | hg19, hg38, mm9, mm10 |
GSE72311_lncrna | long non-coding RNA transcripts from the GSE72311 study | mm10 |
knownGene | A set of UCSC gene predictions based on data from RefSeq, GenBank, CCDS, Rfam, and the tRNA Genes track | hg19, hg38, mm9, mm10 |
lincRNAsTranscripts | Human Body Map lincRNAs (large intergenic non coding RNAs) and TUCPs (transcripts of uncertain coding potential) | hg19, hg38 |
mgcGenes | The Mammalian Gene Collection (MGC) of full-length open reading frames (ORFs) in the genome. | hg19, hg38, mm9, mm10 |
refGene | The NCBI RNA reference sequences collection (RefSeq) | hg19, hg38, mm9, mm10 |
sibGene | Swiss Institute of Bioinformatics cDNA/EST-based gene predictions | hg19, hg38 |
vegaGene | Annotated genes from the Vertebrate Genome Annotation (VEGA) database (Human chr14, 20, 22 only) | hg19, mm9 |