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
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.
General information about this species can be found in Wikipedia.
|Assembly||Sscrofa10.2, INSDC Assembly GCA_000003025.4, Aug 2011|
|Golden Path Length||2,808,525,991|
|Genebuild method||Full genebuild|
|Genebuild started||Sep 2011|
|Genebuild released||May 2012|
|Genebuild last updated/patched||Feb 2014|
Genes and/or transcript that contains an open reading frame (ORF).
|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.
|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.
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.
|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|
|Genscan gene predictions||52,372|