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74 results for “protein-coding genes”
Do 5' regions of human protein-coding genes contain the blueprints for alternative splicing?
<p>Datasets generated during the comparative analysis of multiple transcript isoform genes (MISOG) and single transcript isoform genes (SISOG). All data were based on the raw RefSeq GFF file (version <a href="https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/annotation_releases/109.20210514/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz">GCF_000001405.39</a>).Tables containing the Type CDS corresponds to TER (Translated Exonic Regions) in the manuscript.</p> <p>Code can be found here : <a href="https://github.com/weber8thomas/MISOG_SISOG">[Github]</a></p>
Data from: The evolution of protein-coding gene structure in eukaryotes
<p>Introns are highly prevalent in most eukaryotic genomes. Despite the accumulating evidence for benefits conferred by the possession of introns, their specific roles and functions, as well as the processes shaping their evolution, are still only partially understood. Here we explore the evolution of the eukaryotic gene intron-exon structure by focusing on several key features such as the intron length, the number of introns, and the intron-to-exon ratio of protein-coding genes. We utilize whole genome data from 590 species covering the main eukaryotic taxonomic groups and analyze them within a statistical phylogenetic framework. We found that the basic gene structure differs markedly among the main eukaryotic phyla, with animals, and particularly chordates, displaying intron-rich genes, compared to plants and fungi. Reconstruction of gene structure evolution suggests that these differences had evolved prior to the divergence of the phyla, and have remained mostly conserved within groups. We revisit the previously reported association between the genome size and the mean intron length, and report that the correlation patterns differ considerably among phyla. Our findings suggest that the evolution of introns may be affected by different processes across the eukaryotic tree. The substantial diversity in gene structures may indicate that introns play different molecular and evolutionary roles in different organisms.</p>
Data from: The evolution of protein-coding gene structure in eukaryotes
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Data from: How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher-Wright mutation-selection framework
First principles of population genetics are used to obtain formulae relating the non-synonymous to synonymous substitution rate ratio to the selection coefficients acting at codon sites in protein-coding genes. Two theoretical cases are discussed and two examples from real data (a chloroplast gene and a virus polymerase) are given. The formulae give much insight into the dynamics of non-synonymous substitutions and may inform the development of methods to detect adaptive evolution.
Data from: Successful recovery of nuclear protein-coding genes from small insects in museums using illumina sequencing
In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced.
The GC-content at the 5'ends of human protein-coding genes is undergoing mutational decay
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Data from: How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher-Wright mutation-selection framework
Open the record for dataset details and reuse information.
Data from: Successful recovery of nuclear protein-coding genes from small insects in museums using illumina sequencing
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The RNA exosome shapes the expression of key protein-coding genes
GEO Series GSE147655. Homo sapiens. 13 samples. Type: Other.
Alternative Capture of Noncoding RNAs or Protein-Coding Genes by Herpesviruses to Alter Host T-Cell Function
GEO Series GSE55185. Callithrix jacchus. 9 samples. Type: Expression profiling by high throughput sequencing.
Aegilops tauschii reference genome sequence Aet v5.0 including annotation of small RNAs and reannotation of protein-coding genes
GEO Series GSE169198. Aegilops tauschii. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring [case 2]
GEO Series GSE65452. Homo sapiens. 2 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Expression of protein-coding genes and lncRNAs in brain and other human tissues
GEO Series GSE81410. Homo sapiens. 15 samples. Type: Expression profiling by array; Non-coding RNA profiling by array.
Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring [case 3]
GEO Series GSE65453. Homo sapiens. 3 samples. Type: Genome variation profiling by genome tiling array.
[Gene Expression Training Set] Protein-coding and MicroRNA Biomarkers of Recurrence of Prostate Cancer Following Radical Prostatectomy
GEO Series GSE26022. Homo sapiens. 192 samples. Type: Expression profiling by array.
Mycoplasma genitalium and M. pneumoniae induce a distinct set of protein-coding genes in epithelial cells.
GEO Series GSE179051. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Co-expression of long non-coding RNAs and protein-coding genes in pediatric B-cell acute lymphoblastic leukemia
GEO Series GSE128254. Homo sapiens. 46 samples. Type: Expression profiling by array; Non-coding RNA profiling by array.
CHR11 promotes the production of siRNAs from endogenous protein-coding genes
GEO Series GSE278529. Arabidopsis thaliana. 12 samples. Type: Non-coding RNA profiling by high throughput sequencing.
A daily temporal program for rhythmic expression of protein-coding and non-coding genes in response to light and dark in Synechocystis sp. PCC 6803
GEO Series GSE47482. Synechocystis sp. PCC 6803. 62 samples. Type: Expression profiling by array.
ZC3H4, ARS2, and WDR82 coordinate non-coding transcriptional termination and are opposed by telescripting on protein-coding genes [chip-seq]
GEO Series GSE207416. Homo sapiens. 8 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.