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Leopard assembly and gene annotation

Assembly

The PanPar1.0 assembly was submitted by Ulsan National Institute of Science and Technology on 2016/11/16 . The assembly is on the Scaffold level, consisting of 265,330 assembled into 50,377 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 20,993 while the scaffold N50 is 21,701,857.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_001857705.1

Gene annotation

The leopard (Panthera pardus) /ˈlɛpərd/ is one of the five species in the genus Panthera, a member of the Felidae. The leopard occurs in a wide range in sub-Saharan Africa and parts of Asia and is listed as Vulnerable on the IUCN Red List because leopard populations are threatened by habitat loss and fragmentation, and are declining in large parts of the global range. In Hong Kong, Singapore, Kuwait, Syria, Libya, Tunisia and most likely in Morocco, leopard populations have already been extirpated. Contemporary records suggest that the leopard occurs in only 25% of its historical global range. Leopards are hunted illegally, and their body parts are smuggled in the wildlife trade for medicinal practices and decoration.

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

AssemblyPanPar1.0, INSDC Assembly GCA_001857705.1, Nov 2016
Base Pairs2,478,865,742
Golden Path Length2,578,019,207
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJan 2018
Genebuild releasedJun 2018
Genebuild last updated/patchedJun 2018
Database version94.1

Gene counts

Coding genes19,688
Non coding genes3,900
Small non coding genes3,317
Long non coding genes7
Misc non coding genes576
Pseudogenes1,505
Gene transcripts35,228

Other

Genscan gene predictions51,224

About this species