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Pig assembly and gene annotation


The Sscrofa11.1 assembly of the pig genome was produced in January 2017 by the Swine Genome Sequencing Consortium (SGSC). It consists of 20 chromosomes (1-18, X and Y) and 583 unplaced 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 48,231,277 while the scaffold N50 is 88,231,837. The pig genome sequence has been release under the term of the Toronto Statement (Nature 2009, 461: 168).


Gene annotation

Sscrofa11.1 was annotated using the standard Ensembl automatic gene annotation system, incorporating RNA-Seq data and PacBio long reads provided by the SGSC. The gene annotation process was carried out using a combination of cDNA alignments, protein-to-genome alignments, PacBio long reads and RNA-seq alignments. 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 transcriptomic 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.

PacBio long read data set

Nine tissue samples were sequenced using the PacBio long read sequencing technology, brain, diaphragm, hypothalamus, liver, longissimus muscle, pituitary, small intestine, spleen, thymus. All sets were sequenced using 3' capping and were used to add UTR to gene models and as input source for our lincRNA discovery pipeline.
Furthermore we collapsed the models created to produce a non-redundant set. We did a BLASTp of these models against UniProt proteins of vertabrate species with protein existence level 1 and 2 in order to confirm the open reading frame (ORF). We also checked the splice junctions with the RNA-seq data set. The models with a high coding potential and with full RNA-seq support were used as input for the gene model generation.

The tissue-specific sets of aligned sequences are as follows:

TissueNumber of aligned sequences
Longissimus muscle361864
Small intestine406144

RNASeq data set

In addition to the main set, we have predicted gene models for each tissue type using the RNA-Seq pipeline. We did a BLASTp of these models against UniProt proteins of vertabrate species with protein existence level 1 and 2 in order to confirm the open reading frame (ORF). The best BLAST hit is displayed as a transcript supporting evidence. The data was also used to add UTR to gene models.

The tissue-specific sets of transcript models built using our RNAseq pipeline are as follows:

TissueNumber of gene models
Alveolar macrophages34867
Brain stem35791
Corpus callosum37474
Frontal lobe35119
Kidney cortex35544
Left ventricle33125
Mesenteric lymph node40250
Medulla oblongata42716
Occipital lobe35390
Pituitary gland33800
Skeletal muscle32011

More information

General information about this species can be found in Wikipedia.



AssemblySscrofa11.1, INSDC Assembly GCA_000003025.6, Dec 2016
Base Pairs2,501,912,388
Golden Path Length2,501,912,388
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJan 2017
Genebuild releasedJul 2017
Genebuild last updated/patchedDec 2019
Database version104.111

Gene counts

Coding genes21,303
Non coding genes8,979
Small non coding genes2,165
Long non coding genes6,797
Misc non coding genes17
Gene transcripts63,041


Genscan gene predictions46,573
Short Variants64,310,125
Structural variants224,038

About this species