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 the standard Ensembl automatic gene annotation system, incorporating RNA-Seq data provided by the (SGSC). The annotation process is described in the document below. The Ensembl annotations were then merged with Vega annotations at the transcript level. Transcripts were merged if they shared the same internal exon-intron boundaries (i.e. had identical splicing pattern) with slight differences in the terminal exons allowed. Importantly, all Vega source transcripts were included in the final merged gene set. The Vega annotations comprised manual annotation of 2,000 genes both from Havana and from the Immune Response Annotation Group (IRAG) community annotation initiative, which was performed under the guidance of the Havana group.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblySscrofa10.2, INSDC Assembly GCA_000003025.4, Aug 2011
Database version77.102
Base Pairs3,024,658,544
Golden Path Length

The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).

2,808,525,991
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
Small non coding genes

Small 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 small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.

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 Variants28,719,390
Structural variants85