Btau_4.6.1_chromosomes.fa.gz - This file contains FASTA formatted sequences for chr1-chr29, chrX, chrY and 11661 unassigned scaffolds.
Ensembl75_liftOver_Btau_4.6.1_genes.gff3.gz - This file contains Bovine protein coding genes and non-protein-coding genes predicted on UMD3.1 assembly (Ensembl release 75) which are mapped to Btau_4.6.1 using UCSC liftOver Tool.
Ensembl75_liftOver_Btau_4.6.1_partial_genes.gff3.gz - This file contains genes that did not completely liftOver from UMD3.1 to Btau_4.6.1 assembly.
The following files contain data from NCBI Bos taurus Annotation Release 103. We downloaded the GFF file from NCBI FTP site for the Bos taurus genome and formatted it into individual feature type-based files for our Jbrowse/Apollo database.
RefSeq_Btau_4.6.1_protein_coding.gff3.gz - This file contains protein-coding genes.
RefSeq_Btau_4.6.1_frameshift.gff3.gz - This file contains protein coding genes that are supported by cDNA alignments to the genome assembly, but have translational discrepancies due to assembly errors such as indels.
RefSeq_Btau_4.6.1_microRNA.gff3.gz - This file contains microRNA genes.
RefSeq_Btau_4.6.1_noncoding.gff3.gz - This file contains other non-protein-coding genes.
RefSeq_Btau_4.6.1_pseudogene.gff3.gz - This file contains psuedogenes.
RefSeq_Btau_4.6.1_multitype_protein_coding.gff3.gz - This file contains protein-coding genes that have coding as well as non-coding transcripts.
RefSeq_Btau_4.6.1_multitype_noncoding.gff3.gz - This file contains non-protein-coding genes that have coding as well as non-coding transcripts.
RefSeq_Btau_4.6.1_multitype_frameshift.gff3.gz - This file contains frameshift genes that have coding as well as non-coding transcripts.
Bovine Official Gene Set version 2
Bovine_OGSv2_liftOver_Btau_4.6.1_genes.gff3.gz - This file contains the Bovine Official Gene Set version 2, which includes manual annotations submitted by bovine researchers as part of the Bovine Genome Sequencing Consortium project. Genes predicted on the Btau_4.0 assembly were mapped to Btau_4.6.1 using the UCSC liftOver Tool.
Bovine_OGSv2_liftOver_Btau_4.6.1_partial_genes.gff3.gz - This file contains genes that did not completely liftOver from Btau_4.0 to Btau_4.6.1 assembly.
Bovineqtl_liftOver_Btau_4.6.1_QTL.gff3.gz - This file contains Bovine QTL predicted on Btau_4.0, which are mapped to Btau_4.6.1 using UCSC liftOver Tool.
Animalgenome_Btau_4.6.1_QTL.gff3.gz - This file contains QTL for Btau_4.6.1 assembly as provided by Animalgenome.org. We downloaded the GFF3 file and reformatted it for our JBrowse/GBrowse database.