Sentences with phrase «orthologous orfs»

RESULTS: Transcription of the MAOA gene in rhesus monkeys is modulated by an orthologous polymorphism (rhMAOA - LPR) in its upstream regulatory region.

Of these, 126 genes were orthologous to protein - coding genes in the human genome (hereafter, human BC susceptibility genes, hBCSGs), 70 % of which are previously reported cancer - associated genes, and ∼ 16 % are known BC suppressor genes.

By contrast, Pou5f1 - null mouse embryos maintained the expression of orthologous genes, and blastocyst development was established, but maintenance was compromised.

In the present study, we used a combination of BAC clone contig construction, polymorphism analysis of DNA from congenic strains, and sequence mining of the human orthologous region to generate an integrated map of the Idd10 region on mouse chromosome 3.

Indeed, key aspects of most human disorders can be modeled in experimentally tractable organisms through the analysis of orthologous genes and pathways, using the genetic, biochemical and cell biological toolboxes that have been developed in each model organism.

When orthologous proteins were compared between these two populations, the same pattern emerged — proteins from the smaller populations were more flawed than those from the free - living bacteria of the same species.

Functional annotation was done by comparing the reads against the Clusters of Orthologous Genes (COGs)[45] and TIGRFAMS [46] databases using RPSBLAST [47](E-value cut - off of 10 - 5).

Orthologous ORFs for Lcn16 and Lcn17 are found in the same orientation in the rat genome, but synteny is disrupted around this location in the primate lineage and there are no orthologues present in primates or the human genome.

Using data from the National Center for Integrative Biomedical Informatics (NCIBI)'s MiMI: (Michigan Molecular Interactions) which contains data from IntAct, DIP, BIND and others, we identified conserved and predicted novel protein - protein interactions (interologs or interologues) in human, mouse, fly, worm, and yeast based on interaction of orthologous proteins found in the other organisms.

Rapidly diverging short genes, even when they are evolutionarily orthologous to genes in other species, may be nearly impossible to classify as such.

This is only done for the antibodies corresponding to genes where the mouse and human genes are orthologous.

Shared orthologous clusters produced using OrthoMCL version 1.4 with default parameters.

The new genes, however, also include 119 genes that are 1 - 1 orthologous to genes in P. vivax.

The SEED database was used to associate orthologous functions between the pseudomonad genomes.

For example, Bsl1 itself was highly increased in bsl1 - 1 mutants (corrected P = 0.003), as was a gene encoding a BR C - 6 oxidase orthologous to brassinosteroid deficient1 (brd1) from maize (Makarevitch et al., 2012) and rice (Hong et al., 2002)(SvBrd1; Sevir.9 G171700).

Pepper explains, «One of the exciting things about this approach is that it employs a widely used, well - supported, off - the - shelf bioinformatics software known as Stacks (written by Julian Catchen at the University of Oregon) as a «filter» to enrich for pairs of fragments that are likely to be alleles of a single, orthologous region, rather than paralogs or homeologs.»

The team then filtered these reads to enrich for orthologous DNA fragments.

Open Reading Frame E3 - 10.9 K of Subspecies B1 Human Adenoviruses Encodes a Family of Late Orthologous Proteins That Vary in Their Predicted Structural Features and Subcellular Localization.

Positive selection in the human genome inferred from human — chimp — mouse orthologous gene alignments.

According to Pepper, «A problem arises when our computational methods accidentally align DNA regions that are duplicated within the genomes of the plants being studied, rather than mapping the orthologous regions between the plants.»

Positive selection in the human genome inferred from human — chimp — mouse orthologous gene alignments Clark, A. G., S. Glanowski, R. Nielsen, P. Thomas et al. 2003.

Co-developed a method for determining mammalian orthologous genes and their intron / exon boundaries using genome and mRNA data.

Co-developed a method for determining orthologous genes in prokaryotes that can differentiate close paralogs using gene neighborhood context.

Inferring nonneutral evolution from human - chimp - mouse orthologous gene trios.

Of 3671 barn owl long terminal repeat TE insertion loci orthologous in all of the bird genomes, 61 were informative for owls among core landbirds and showed two dominant exclusive TE topologies: (i) an owl + Accipitrimorphae topology, as seen in the MP - EST * TENT; and (ii) an owl + Coraciimorphae topology that excludes mousebird, as seen in the UCE tree (Fig. 3G compared to Figs. 3B and 4B).

S4, A and B), despite the outgroups having only ~ 30 % orthologous sequences in the TENT alignment (e.g., fig.

From these efforts, we identified a high - quality orthologous gene set across avian species, consisting of exons from 8251 syntenic protein - coding genes (~ 40 % of the proteome), introns from 2516 of these genes, and a nonoverlapping set of 3769 ultraconserved elements (UCEs) with ~ 1000 bp of flanking sequences.

Further exploring data amount, we used the assembled ~ 1.1 - billion - bp chicken genome (40) as a reference to generate a 322 - million - bp MULTIZ alignment of putatively orthologous genome regions across all species, comprising ~ 30 % of an average assembled avian genome and corresponding to the maximal orthologous sequence obtainable across all orders under our homology criteria (SM3).

«However, because SIF - seq only requires DNA sequence from a mammal and can be used in a variety of cell types, it should be possible to compare the neuronal enhancers present in a large genomic region from human to the neuronal enhancers present in the orthologous chimpanzee region.