Naked mole-rat female assembly and gene annotation

Assembly

The HetGla_female_1.0 assembly was submitted by Broad Institute on 2012/02/17 . The assembly is on the Scaffold level, consisting of 114,653 assembled into 4,229 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 47,778 while the scaffold N50 is 20,532,749 The genome assembly represented here corresponds to GenBank Assembly ID: GCA_000247695.1

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000247695.1

Gene annotation

The naked mole-rat (Heterocephalus glaber), also known as the sand puppy or desert mole rat, is a burrowing rodent closely related to the blesmols, native to parts of East Africa, and is the only species currently classified in the genus Heterocephalus. The genus is classified as being in the family Bathyergidae or in its own family, Heterocephalidae. The naked mole-rat, the Damaraland mole-rat, and Mechow's mole-rat are eusocial mammals, the highest classification of sociality. It has a highly unusual set of physical traits that enable it to thrive in an otherwise harsh underground environment; it is the only mammalian thermoconformer, almost entirely ectothermic (cold-blooded) in how it regulates body temperature.

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

AssemblyHetGla_female_1.0, INSDC Assembly GCA_000247695.1, Feb 2012
Base Pairs2,314,771,103
Golden Path Length2,618,204,639
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2016
Genebuild releasedJul 2017
Genebuild last updated/patchedJul 2017
Database version90.1

Gene counts

Coding genes20,774
Non coding genes10,396
Small non coding genes2,908
Long non coding genes6,664
Misc non coding genes824
Pseudogenes636
Gene transcripts41,385

Other

Genscan gene predictions54,718

About this species