Threespine stickleback v. 5.0.1 assembly
The v. 5.0.1 assembly contains the original published Y (total length 15,866,398 bp) for users that wish to work with this chromosome.
It is recommended that users work with the v. 5 assembly.
The v. 5 annotations are compatible with the v. 5.0.1 assembly.
Threespine stickleback v. 5 assembly
The v. 5 genome published in 2021 contains a modified Y chromosome (total length 15,859,692 bp). A 6706 bp segment that contained repetitive elements was removed from the end of the chromosome. 269 bp was also added to one of the gaps between contigs. The remainder of the Y chromosome is identical to the published version (Peichel et al. 2020. Genome Biology).
- The v. 5 genome is also annotated and available in a genome browser by NCBI.
Ensembl annotations (release 95)
MAKER gene annotations within newly closed gaps in the v5 genome
MAKER gene annotations on the Y chromosome
Repeat annotations
Threespine stickleback v. 4 (2017) assembly
The genome fasta sequence includes the published Y chromosome (total length 15,866,398 bp; Peichel et al. 2020. Genome Biology).
Ensembl annotations (release 95)
Repeat annotations
LiftOver Files
v. 1 Ensembl (with scaffolds; Jones et al. 2012) to v. 5
v. 1 UCSC (with chr. Un; Jones et al. 2012) to v. 5
v. 2 (Roesti et al. 2013) to v. 5
v. 3 (Glazer et al. 2015) to v. 5
v. 4 (Peichel et al. 2017) to v. 5