Lesser Egyptian jerboa assembly and gene annotation

Assembly

The JacJac1.0 assembly was submitted by Broad Institute on 2012/07/30 . The assembly is on the Scaffold level, consisting of 337,362 assembled into 10,898 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 15,675 while the scaffold N50 is 22,080,993 The genome assembly represented here corresponds to GenBank Assembly ID: GCA_000280705.1

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000280705.1

Gene annotation

The lesser Egyptian jerboa الجربوع (Jaculus jaculus) is a small rodent of Africa and the Middle East. Its diet consists mainly of seeds and grasses, however the Jerboa needs very little water to survive.

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

AssemblyJacJac1.0, INSDC Assembly GCA_000280705.1, Jul 2012
Base Pairs2,470,267,327
Golden Path Length2,835,250,225
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedOct 2016
Genebuild releasedFeb 2017
Genebuild last updated/patchedFeb 2017
Database version90.10

Gene counts

Coding genes17,845
Non coding genes6,267
Small non coding genes4,996
Long non coding genes21
Misc non coding genes1,250
Pseudogenes321
Gene transcripts31,768

Other

Genscan gene predictions54,743

About this species