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Zebra finch assembly and gene annotation

Assembly

The bTaeGut1_v1.p assembly was submitted by Vertebrate Genomes Project on May 2019. The assembly is on chromosome level, consisting of 444 contigs assembled into 135 scaffolds. From these sequences, 33 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 11,998,827 while the scaffold N50 is 70,430,603.

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

AssemblybTaeGut1_v1.p, INSDC Assembly GCA_003957565.2, May 2019
Base Pairs1,057,995,280
Golden Path Length1,057,995,280
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2019
Genebuild releasedDec 2019
Genebuild last updated/patched
Database version100.12

Gene counts

Coding genes16,619
Non coding genes5,395
Small non coding genes634
Long non coding genes4,759
Misc non coding genes2
Pseudogenes132
Gene transcripts38,869

Other

Genscan gene predictions37,466
Short Variants1,581,781

About this species

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