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174 results for “gene architecture”
Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow
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Data from: Impact of male trait exaggeration on sex-biased gene expression and genome architecture in a water strider
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Data from: The genetic architecture of reproductive isolation during speciation-with-gene-flow in lake whitefish species pairs assessed by RAD sequencing
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The genomic architecture of the passerine MHC region: high repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes
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Data from: Deciphering the genomic architecture of the stickleback brain with a novel multi-locus gene-mapping approach
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Data from: Genes and QTLs controlling inflorescence and stem branch architecture in Leymus (Poaceae: Triticeae) wildrye
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Data from: Genome divergence and the genetic architecture of barriers to gene flow between Lycaeides idas and L. melissa
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Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow
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Data from: Gene expression levels are correlated with synonymous codon usage, amino acid composition and gene architecture in the red flour beetle, Tribolium castaneum
Gene expression levels correlate with multiple aspects of gene sequence and gene structure in phylogenetically diverse taxa suggesting an important role of gene expression levels in the evolution of protein-coding genes. Here we present results of a genome-wide study of the influence of gene expression on synonymous codon usage, amino acid composition and gene structure in the red flour beetle, Tribolium castaneum. Consistent with the action of translational selection, we find that synonymous codon usage bias increases with gene expression. However, the correspondence between tRNA gene copy number and optimal codons is weak. At the amino acid level, translational selection is suggested by the positive correlation between tRNA gene numbers and amino acid usage which is stronger for highly expressed genes. In addition, there is a clear trend for increased use of metabolically cheaper, less complex, amino acids as gene expression increases. tRNA gene numbers also correlate negatively with amino acid size/complexity score indicating the coupling between translational selection and selection to minimize the use of large/complex amino acids. Interestingly, the correlation between tRNA gene numbers and amino acid size/complexity score appears to be widespread given our analyses of 10 additional genomes and might be explained by selection against negative consequences of protein misfolding. At the level of gene structure, three major trends are detected 1) CDS length increases across low and intermediate expression levels but decreases in highly expressed genes; 2) the average intron size shows the opposite trend, first decreasing with expression, followed by a slight increase in highly expressed genes and 3) intron density remains nearly constant across all expression levels. These changes in gene architecture are only in partial agreement with selection favoring reduced cost of biosynthesis.
Data from: Genetic architecture and functional characterization of genes underlying the rapid diversification of male external genitalia between Drosophila simulans and Drosophila mauritiana
Male sexual characters are often among the first traits to diverge between closely related species and identifying the genetic basis of such changes can contribute to our understanding of their evolutionary history. However, little is known about the genetic architecture or the specific genes underlying the evolution of male genitalia. The morphology of the claspers, posterior lobes and anal plates exhibit striking differences between Drosophila mauritiana and Drosophila simulans. Using QTL and introgression-based high-resolution mapping, we identified several small regions on chromosome arms 3L and 3R that contribute to differences in these traits. However, we found that the loci underlying the evolution of clasper differences between these two species are independent from those that contribute to posterior lobe and anal plate divergence. Furthermore, while most of the loci affect each trait in the same direction and act additively, we also found evidence for epistasis between loci for clasper bristle number. In addition, we conducted an RNAi screen in D. melanogaster to investigate if positional and expression candidate genes located on chromosome 3L, are also involved in genital development. We found that six of these genes, including components of Wnt signaling and male-specific lethal 3 (msl3), regulate the development of genital traits consistent with the effects of the introgressed regions where they are located and that thus represent promising candidate genes for the evolution these traits.
Dataset: The unusual gene architecture of polyubiquitin is created by dual-specific splice sites
<p>Data for the research paper "The unusual gene architecture of polyubiquitin is created by dual-specific splice sites".</p>
Data from: Genetic architecture and functional characterization of genes underlying the rapid diversification of male external genitalia between Drosophila simulans and Drosophila mauritiana
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Data from: Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula
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Data from: Gene expression levels are correlated with synonymous codon usage, amino acid composition and gene architecture in the red flour beetle, Tribolium castaneum
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PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [RNA-Seq]
GEO Series GSE183297. Homo sapiens. 30 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq: Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci
GEO Series GSE54952. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant common complex traits (RNA-Seq)
GEO Series GSE152097. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Disentangling the architectural and non-architectural functions of CTCF and cohesin in global gene regulation [EU-Seq]
GEO Series GSE262520. Mus musculus. 60 samples. Type: Other.
Cohesin-based chromatin interactions enable regulated gene expression within pre-existing architectural compartments.
GEO Series GSE48763. Mus musculus. 13 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [ATAC-Seq II]
GEO Series GSE188668. Homo sapiens. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.