Number of genes

Value 23300 unitless
Organism Sea urchin Strongylocentrotus purpuratus
Reference Sea Urchin Genome Sequencing Consortium and researchers, The genome of the sea urchin Strongylocentrotus purpuratus. Science. 2006 Nov 10 314(5801):941-52. abstract, p. 942 left column 3rd paragraph & right column 2nd paragraph & p.950 middle column 2nd paragraphPubMed ID17095691
Method "To estimate the number of genes in the S. purpuratus genome, researchers began with the 28,900 gene models in the official gene set (OGS) and reduced this by the 5% redundancy found by mapping to the v 2.0 assembly, then increased it by a few percent for the new genes observed in the Ensembl set from the v 2.0 assembly compared with v 0.5. From manual analysis of well-characterized gene sets (e.g., ciliary, cell cycle control, and RNA metabolism genes), they estimated that, in addition to redundancy, another 25% of the genes in the OGS were fragments, pseudogenes, or otherwise not valid. Finally, whole-genome tiling microarray analysis showed 10% of the transcriptionally active regions (long open reading frames, not small RNAs) were not represented by genes in the OGS. Taken together, this analysis gave an estimate of about 23,300 genes for S. purpuratus. Information on all annotated genes can be found at ( link not active as of March 8th 2015)."
Comments "The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes." "The sea urchin is estimated to have 23,300 genes with representatives of nearly all vertebrate gene families, although often the families are not as large as in vertebrates." "The overall trends in gene structure were similar to those seen in the human genome. The statistics of the Ensembl predictions from the whole-genome shotgun (WGS) assembly revealed an average of 8.3 exons and 7.3 introns per transcript (see SOM). The average gene length was 7.7 kb with an average primary transcript length of 8.9 kb. A broad distribution of all exon lengths peaked at around 100 to 115 nucleotides, whereas that for introns at around 750 nucleotides. The smaller average intron size relative to humans' was consistent with the trend that intron size is correlated with genome size." "[Researcgers'] estimate of 23,300 genes is similar to estimates for vertebrates, despite the fact that two whole-genome duplications are believed to have occurred in the chordate lineage after divergence from the lineage leading to the echinoderms (refs 25–27)." See BNID 105517
Entered by Uri M
ID 105518