Naked mole-rat male (Naked_mole-rat_paternal)

Naked mole-rat male assembly and gene annotation

Assembly

The Naked mole-rat paternal assembly was submitted by hospital for sick children on July 2022. The assembly is on chromosome level, consisting of 2,350 contigs assembled into 32 scaffolds. From these sequences, 30 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 2,890,005 while the scaffold N50 is 94,825,129.

Other assemblies

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

AssemblyNaked_mole-rat_paternal, INSDC Assembly GCA_944319725.1, Jul 2022
Base Pairs2,499,457,497
Golden Path Length2,499,457,497
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2022
Genebuild released
Genebuild last updated/patchedSep 2022
Database version111.1

Gene counts

Coding genes23,343
Non coding genes10,427
Small non coding genes2,554
Long non coding genes7,836
Misc non coding genes37
Pseudogenes1,344
Gene transcripts71,945