Asiatic black bear (ASM966005v1)

Asiatic black bear assembly and gene annotation

Assembly

The ASM966005v1 assembly was submitted by Northwestern Polytechnical University on November 2019. The assembly is on scaffold level, consisting of 54,646 contigs assembled into 24,973 scaffolds. 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 145,966 while the scaffold N50 is 26,803,000.

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

AssemblyASM966005v1, INSDC Assembly GCA_009660055.1, Nov 2019
Base Pairs2,373,594,928
Golden Path Length2,373,594,928
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2019
Genebuild releasedApr 2020
Genebuild last updated/patchedDec 2019
Database version111.1

Gene counts

Coding genes20,126
Non coding genes2,637
Small non coding genes2,210
Long non coding genes411
Misc non coding genes16
Pseudogenes447
Gene transcripts39,661

Other

Genscan gene predictions66,076