Pig assembly and gene annotation

Assembly

The Sscrofa10.2 assembly of the pig genome was produced in August 2011 by the Swine Genome Sequencing Consortium (SGSC). It consists of 20 chromosomes (1-18, X and Y) and 4562 unplaced scaffolds. This genome assembly has GCA_000003025.4 as its GenBank assembly accession.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000003025.4

Gene annotation

Sscrofa10.2 was annotated using a standard Ensembl mammalian genebuild pipeline, incorporating RNA-Seq data provided by the (SGSC). The annotation process is described in this document. When the annotation was completed, the gene set contained the following: 21,640 protein coding genes, 380 pseudogenes and 2,965 ncRNAs.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblySscrofa10.2, INSDC Assembly GCA_000003025.4, Aug 2011
Database version75.102
Base Pairs3,024,658,544
Golden Path Length2,808,525,991
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedSep 2011
Genebuild releasedMay 2012
Genebuild last updated/patchedFeb 2014

Gene counts

Coding genes

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

21,630
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.

2,989
Long non coding genes

Long non coding genes are usually greater than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as long non coding genes: 3prime_overlapping_ncrna, ambiguous_orf, antisense, antisense_RNA, lincRNA, ncrna_host, non_coding, non_stop_decay, processed_transcript, retained_intron, sense_intronic, sense_overlapping. The majority of the long non coding genes in Ensembl are annotated manually by HAVANA.

135
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.

568
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.30,585

Other

Genscan gene predictions52,372
Short Variants28,719,264
Structural variants218

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