Comprehensive gene annotation |
CHR |
- It contains the comprehensive gene annotation on the reference chromosomes only
- This is the main annotation file for most users
|
GTF
GFF3
|
Comprehensive gene annotation |
ALL |
- It contains the comprehensive gene annotation on the reference chromosomes, scaffolds, assembly patches and alternate loci (haplotypes)
- This is a superset of the main annotation file
|
GTF
GFF3
|
Comprehensive gene annotation |
PRI |
- It contains the comprehensive gene annotation on the primary assembly (chromosomes and scaffolds) sequence regions
- This is a superset of the main annotation file
|
GTF
GFF3
|
Basic gene annotation |
CHR |
- It contains the basic gene annotation on the reference chromosomes only
- This is a subset of the corresponding comprehensive annotation, including only those transcripts tagged as 'basic' in every gene
|
GTF
GFF3
|
Basic gene annotation |
ALL |
- It contains the basic gene annotation on the reference chromosomes, scaffolds, assembly patches and alternate loci (haplotypes)
- This is a subset of the corresponding comprehensive annotation, including only those transcripts tagged as 'basic' in every gene
|
GTF
GFF3
|
Long non-coding RNA gene annotation |
CHR |
- It contains the comprehensive gene annotation of lncRNA genes on the reference chromosomes
- This is a subset of the main annotation file
|
GTF
GFF3
|
PolyA feature annotation |
CHR |
- It contains the polyA features (polyA_signal, polyA_site, pseudo_polyA) manually annotated by HAVANA on the reference chromosomes
- This dataset does not form part of the main annotation file
|
GTF
GFF3
|
Consensus pseudogenes predicted by the Yale and UCSC pipelines |
CHR |
- 2-way consensus (retrotransposed) pseudogenes predicted by the Yale and UCSC pipelines, but not by HAVANA, on the reference chromosomes
- This dataset does not form part of the main annotation file
|
GTF
GFF3
|
Predicted tRNA genes |
CHR |
- tRNA genes predicted by ENSEMBL on the reference chromosomes using tRNAscan-SE
- This dataset does not form part of the main annotation file
|
GTF
GFF3
|