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Panda assembly and gene annotation

The giant panda (Ailuropoda melanoleuca) is a bear native to south central China. For many decades, the precise taxonomic classification of the giant panda was under debate because it shares characteristics with both bears and raccoons. However, molecular studies indicate the giant panda is a true bear, part of the family Ursidae. These studies show it differentiated early (about 19 million years ago) from the main ursine stock; since it is the most basal member of the group, it is equidistant from all other extant ursids. The giant panda has been referred to as a living fossil.


ailMel1 (GCA_000004335.1) is an assembly of the giant panda, sequenced using a three-year-old female panda at China's Chengdu breeding center. The genome sequencing and assembly are provided by the Bejing Genomics Institute (BGI).

The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 size of the scaffolds is 1.3Mb. The total length of all scaffolds is 2.3Gb, for a genome size estimated to be 2.4Gb.

Gene annotation

The gene set for panda was built using the Ensembl pipeline. Gene models are based on genewise alignments of mammal proteins as well as genetically distance proteins from other species, including most vertebrate proteins from Uniprot. Additionally, dog and human proteins were aligned using exonerate.

Potentially missing predictions and partial gene predictions were identified by examining the orthologs, which were then used to build new gene models.

More information

General information about this species can be found in Wikipedia.



AssemblyailMel1, INSDC Assembly GCA_000004335.1, Jul 2009
Base Pairs2,245,312,831
Golden Path Length2,299,509,015
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJan 2010
Genebuild releasedOct 2010
Genebuild last updated/patchedDec 2011
Database version100.1

Gene counts

Coding genes19,343
Non coding genes3,141
Small non coding genes2,783
Misc non coding genes358
Gene transcripts25,055


Genscan gene predictions52,637

About this species