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Hybrid - Bos Indicus assembly and gene annotation

Assembly

The UOA_Brahman_1 assembly was submitted by University of Adelaide on November 2018. The assembly is on chromosome level, consisting of 1,552 contigs assembled into 1,250 scaffolds. From these sequences, 30 chromosomes have been built. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 26,764,281 while the scaffold N50 is 104,466,507.

Click here (Koren et al. 2018) for the corresponding publication on the genome/assembly.

Gene annotation

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments.
Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold.
Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome.
lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

In accordance with the Fort Lauderdale Agreement, please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyUOA_Brahman_1, INSDC Assembly GCA_003369695.2, Nov 2018
Base Pairs2,680,953,056
Golden Path Length2,680,953,056
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedDec 2018
Genebuild releasedJun 2019
Genebuild last updated/patchedMar 2019
Database version100.1

Gene counts

Coding genes22,256
Non coding genes7,056
Small non coding genes3,286
Long non coding genes3,384
Misc non coding genes386
Pseudogenes598
Gene transcripts54,700

Other

Genscan gene predictions45,745

About this species

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