List of genomic annotations per species as GRanges objects. The human annotation is the GTF of Hg38 GENCODE release 32 primary assembly, while the gorilla and cynomolgus macaque annotations were created by transferring the human annotation onto the gorGor6 and macFas6 genomes via the tool Liftoff (https://github.com/agshumate/Liftoff). Each annotation was subsetted for the 300 genes that feature in this example dataset.
Format
A named list of 3 GRanges objects. Each object has 8 columns.
Attributes:
- seqnames
Chromosome or contig name.
- start
Genomic start location.
- end
Genomic end location.
- width
Width of the feature in base pairs.
- strand
Genomic strand ("+" or "-").
- source
The prediction program or public database where the annotations came from.
- type
Feature type (gene, transcript, exon, CDS, UTR, start_codon, stop_codon or Selenocysteine).
- score
The degree of confidence in the feature's existence and coordinates.
- phase
One of '0', '1' or '2'. '0' means that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on.
- gene_id
Unique identifier of the gene.
- gene_name
Name of the gene.
- transcript_id
Unique identifier of the transcript.
- transcript_name
Name of the transcript.
Source
<ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.primary_assembly.annotation.gtf.gz>, <https://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/bigZips/gorGor6.fa.gz>, <https://ftp.ensembl.org/pub/release-109/fasta/macaca_fascicularis/dna/Macaca_fascicularis.Macaca_fascicularis_6.0.dna_sm.toplevel.fa.gz>