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Pseudogene

About: Pseudogene is a research topic. Over the lifetime, 5528 publications have been published within this topic receiving 336634 citations. The topic is also known as: Ψ & pseudogenes.


Papers
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Journal ArticleDOI
TL;DR: The misconception that a gene in E. coli whose primary name starts with ‘y’ is unannotated is resolved, and the value of the y-ome is discussed for systematic improvement ofE.
Abstract: Experimental studies of Escherichia coli K-12 MG1655 often implicate poorly annotated genes in cellular phenotypes. However, we lack a systematic understanding of these genes. How many are there? What information is available for them? And what features do they share that could explain the gap in our understanding? Efforts to build predictive, whole-cell models of E. coli inevitably face this knowledge gap. We approached these questions systematically by assembling annotations from the knowledge bases EcoCyc, EcoGene, UniProt and RegulonDB. We identified the genes that lack experimental evidence of function (the 'y-ome') which include 1600 of 4623 unique genes (34.6%), of which 111 have absolutely no evidence of function. An additional 220 genes (4.7%) are pseudogenes or phantom genes. y-ome genes tend to have lower expression levels and are enriched in the termination region of the E. coli chromosome. Where evidence is available for y-ome genes, it most often points to them being membrane proteins and transporters. We resolve the misconception that a gene in E. coli whose primary name starts with 'y' is unannotated, and we discuss the value of the y-ome for systematic improvement of E. coli knowledge bases and its extension to other organisms.

102 citations

Journal ArticleDOI
05 Jun 2008-Nature
TL;DR: Pseudogenes constitute many of the non-coding DNA sequences that make up large parts of genomes, and it now emerges that some of them have active regulatory roles.
Abstract: Pseudogenes constitute many of the non-coding DNA sequences that make up large parts of genomes Once considered merely protein fossils, it now emerges that some of them have active regulatory roles

102 citations

Journal ArticleDOI
TL;DR: Complementary DNA clones corresponding to the 70 and 82 kDa subunits of soluble guanylyl cyclase from human adult brain have been isolated and sequenced and demonstrated the existence of a novel large subunit isoform for soluble guanine cyclase in human tissues.

102 citations

Journal ArticleDOI
TL;DR: The evidence for and against pseudogene functionality are examined, it is argued that the time is ripe for revising the definition of a pseudogene, and a classification system is suggested to accommodate pseudogenes with various levels of functionality.

102 citations

Journal ArticleDOI
17 Dec 2004-Science
TL;DR: Coalescent simulations indicate that ancillary morphological innovations associated with self-pollination can evolve rapidly after the inactivation of the self-incompatibility response, and suggest that the post-Pleistocene expansion of A. thaliana from glacial refugia may have been associated with this adaptive event.
Abstract: The shift to self-pollination is one of the most prevalent evolutionary transitions in flowering plants. In the selfing plant Arabidopsis thaliana, pseudogenes at the SCR and SRK self-incompatibility loci are believed to underlie the evolution of self-fertilization. Positive directional selection has driven the evolutionary fixation of pseudogene alleles of SCR, leading to substantially reduced nucleotide variation. Coalescent simulations indicate that this adaptive event may have occurred very recently and is possibly associated with the post-Pleistocene expansion of A. thaliana from glacial refugia. This suggests that ancillary morphological innovations associated with self-pollination can evolve rapidly after the inactivation of the self-incompatibility response.

101 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
2023120
2022250
2021123
2020160
2019119
2018127