The low number of pseudogenes
and IS elements indicates that this strain has not undergone niche adaptation, and most likely is an opportunistic pathogen (36-38).
Possible roles of the pseudogenes
of Salmonella typhimurium.
A new study led by the Spanish National Cancer Research Centre (CNIO) reveals that up to 20% of genes classified as coding (those that produce the proteins that are the building blocks of all living things) may not be coding after all because they have characteristics that are typical of non-coding or pseudogenes
(obsolete coding genes).
While looking into p53, the researchers found a pseudogene
, called leukemia inhibition factor 6 (LIF6).
STRC is tandemly duplicated, leading to a second nonfunctional copy or pseudogene
,pSTRC, with 98.9% homology across the entire locus, 99% identity in the coding sequence, and 100% identity in the first half (exons 1-15) of the STRC gene (14).
After analyzing DPPA2 gene in different databases and a survey for its pseudogenes
, cloning primer set1 was designed using GeneRunner software version 3.05 (Hastings Software Inc., Hastings, NY, USA) and checked forprobable hairpins, dimers, GC percentage and Tm.
Francisco Carter, "Pseudogenes
: pseudo-functional or key regulators in health and disease?," RNA, vol.
To comparatively describe the differences between type A and type B genomes, we first looked for genes that are putatively specific to each type, whose orthologs were apparently lost or converted into pseudogenes
in all the genomes of the opposite type (Table S4).
Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes
Nuclear insertion of mitochondrial pseudogenes
(numts) represents a cytoplasmic mitochondrial DNA sequence that has naturally been integrated into an organism's nuclear genome over an evolutionary timescale, giving rise to nDNA sequences of mitochondrial origin (Lopez et al., 1994).
Based on the validation results and the technical limitations of NGS, variants in homopolymer regions, indels more than 5 bp in size, genes with high homology to pseudogenes
or within repetitive regions, and exon level copy number variation were determined to be beyond the reportable range of this assay and thus were excluded for calculation of sensitivity and specificity.
Organization and evolution of the flavin-containing mono-oxygenase genes of human and mouse identification of novel gene and pseudogene