Panda assembly and gene annotation

Assembly

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.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000004335.1

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.

Statistics

Summary

AssemblyailMel1, INSDC Assembly GCA_000004335.1, Jul 2009
Database version75.1
Base Pairs2,245,312,831
Golden Path Length2,299,509,015
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedJan 2010
Genebuild releasedOct 2010
Genebuild last updated/patchedDec 2011

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

19,343
Short non coding genes

Short non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as short non coding genes: miRNA, miscRNA, rRNA, tRNA, ncRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, and also the pseudogenic form of these biotypes. The majority of the short non coding genes in Ensembl are annotated automatically by our ncRNA pipeline.

3,141
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

778
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.25,055

Other

Genscan gene predictions52,637

InterPro Hits