Ψ NYX - Physeter catodon

Reference Gene:
Job_ID:
Curator:
GlossID Species Gene Loss Mechanism Loss Type Lineage Specific Evidence Accession Nr.
GL_VMRP4G Physeter catodon Gene deletion Full No Genomic

Statements

Type Excerpt DOI
Functional "eye-enriched visual perception genes" 10.1093/icb/icy004
Methodology & Validation "Absent BLAST hits (i.e., no curated mRNA or gene model available) were likewise treated as providing evidence of gene loss, either through whole gene deletion or degradation to the point of insufficient recognizable homology. However, a lack of BLAST hits and predicted pseudogenes can also be the result of sequencing, assembly, and/or gene model construction errors or unfixed variants. As such, I analyzed two different datasets described as “possible gene losses” and “probable pseudogenes”, respectively. The former assumes all predicted pseudogenes (“low quality proteins”) and absent BLAST results are representations of lost/inactivated genes." 10.1093/icb/icy004

Curator Observations

Only “probable pseudogenes” defined as genes tagged with “low quality protein” containing multiple inactivating mutations and genes with absent BLAST results were collected from this publication, following the authors assumption “that a gene with multiple putative inactivating mutations is less likely to results from unfixed variants or sequencing or assembly errors”.