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Paramormyrops kingsleyae assembly and gene annotation

Assembly

The PKINGS_0.1 assembly was submitted by Michigan State University on January 2018. The assembly is on scaffold level, consisting of 47,999 contigs assembled into 4,667 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 37,656 while the scaffold N50 is 1,731,158.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_002872115.1

Gene annotation

Paramormyrops is a genus of elephantfish in the family Mormyridae from Africa.

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

AssemblyPKINGS_0.1, INSDC Assembly GCA_002872115.1, Jan 2018
Base Pairs799,421,083
Golden Path Length799,421,083
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes24,792
Non coding genes860
Small non coding genes836
Long non coding genes3
Misc non coding genes21
Pseudogenes40
Gene transcripts42,977

Other

Genscan gene predictions45,140

About this species