ArticleGenome research2000
Reverse transcriptase-polymerase chain reaction validation of 25 "orphan" genes from Escherichia coli K-12 MG1655.
Article in Genome research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
11 citing papers in PubMed, 31 citations in OpenAlex.
- Folding Optimization In Vivo Uncovers New Chaperones.Journal of molecular biology · 2015Article
- Improved detection of Escherichia coli and coliform bacteria by multiplex PCR.BMC biotechnology · 2015Article
- Why so many unknown genes? Partitioning orphans from a representative transcriptome of the lone star tick Amblyomma americanum.BMC genomics · 2013Article
- Structural features and the persistence of acquired proteins.Proteomics · 2008Article
- Identification and investigation of ORFans in the viral world.BMC genomics · 2008Article
- The 2-oxoacid dehydrogenase multienzyme complex of Haloferax volcanii.Extremophiles : life under extreme conditions · 2008Article
- Large-scale comparative genomic ranking of taxonomically restricted genes (TRGs) in bacterial and archaeal genomes.PloS one · 2007Article
- On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer.BMC evolutionary biology · 2006Article
- Unravelling the ORFan Puzzle.Comparative and functional genomics · 2003Article
- The source of laterally transferred genes in bacterial genomes.Genome biology · 2003Article
- Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite the accumulation of sequence information sampling from a broad spectrum of phyla, newly sequenced genomes continue to reveal a high proportion (50%-30%) of "uncharacterized" genes, including a significant number of strictly "orphan" genes, i.e., putative open reading frames (ORFs) without any resemblance to previously determined protein-coding sequences. Most genes found in databases have only been predicted by computer methods and have never been experimentally validated. Although theoretical evolutionary arguments support the reality of genes when homologs are found in a variety of distant species, this is not the case for orphan genes. Here, we report the direct reverse transcriptase-polymerase chain reaction assay of 25 strictly orphan ORFs of Escherichia coli. Two growth conditions, exponential and stationary phases, were tested. Transcripts were identified for a total of 19 orphan genes, with 2 genes found to be expressed in only one of the two growth conditions. Our results suggest that a vast majority of E. coli ORFs presently annotated as "hypothetical" correspond to bona fide genes. By extension, this implies that randomly occurring "junk" ORFs have been actively counter selected during the evolution of the dense E. coli genome.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.