Upper Galilee mountains blind mole rat assembly and gene annotation

Assembly

The S.galili_v1.0 assembly was submitted by BGI on 2014/06/05 . The assembly is on the Scaffold level, consisting of 356,097 assembled into 154,976 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 30,353 while the scaffold N50 is 3,618,479 The genome assembly represented here corresponds to GenBank Assembly ID: GCA_000622305.1

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000622305.1

Gene annotation

The Upper Galilee Mountains blind mole-rat (Spalax galili) is an extant species of subterranean rodent within the family Spalacidae, indigenous to Upper Galilee in northern Israel. Following the identification of S. galili in 2001, Nevo et al. recorded specimens in the vicinity surrounding the Kerem Ben Zimra settlement.

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

AssemblyS.galili_v1.0, INSDC Assembly GCA_000622305.1, May 2014
Base Pairs2,913,431,996
Golden Path Length3,061,408,210
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedOct 2016
Genebuild releasedFeb 2017
Genebuild last updated/patchedFeb 2017
Database version90.10

Gene counts

Coding genes18,647
Non coding genes5,623
Small non coding genes4,523
Long non coding genes267
Misc non coding genes833
Pseudogenes366
Gene transcripts32,861

Other

Genscan gene predictions69,389

About this species