Interpretation, Stratification and Evidence for Sequence Variants Affecting mRNA Splicing in Complete Human Genome Sequences

Abstract The completion of human genome sequences and the advancement of next-generation sequencing technologies have engendered a clear understanding of all human genes. Overlapping genes are usually observed in compact genomes, such as those of bacteria and viruses. Notably, overlapping protein-coding genes do exist in human genome sequences. Accordingly, we used the current Ensembl gene annotations to identify overlapping human protein-coding genes. We analysed 19,200 well-annotated protein-coding genes and determined that 4,951 protein-coding genes overlapped with their adjacent genes. Approximately a quarter of all human protein-coding genes were overlapping genes. We observed different clusters of overlapping protein-coding genes, ranging from two genes (paired overlapping genes) to 22 genes. We also divided the paired overlapping protein-coding gene groups into four subtypes. We found that the divergent overlapping gene subtype had a stronger expression association than did the subtypes of 5ʹ-tandem overlapping and 3ʹ-tandem overlapping genes. The majority of paired overlapping genes exhibited comparable coincidental tissue expression profiles; however, a few overlapping gene pairs displayed distinctive tissue expression association patterns. In summary, we have carefully examined the genomic features and distributions about human overlapping protein-coding genes and found coincidental expression in tissues for most overlapping protein-coding genes.

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Predicting Coding Potential from Genome Sequence: Application to Betaherpesviruses Infecting Rats and Mice

Journal of Virology ◽

10.1128/jvi.79.12.7570-7596.2005 ◽

2005 ◽

Vol 79 (12) ◽

pp. 7570-7596 ◽

Cited By ~ 46

Author(s):

Luciano Brocchieri ◽

Thomas N. Kledal ◽

Samuel Karlin ◽

Edward S. Mocarski

Keyword(s):

Genome Annotation ◽

Mrna Splicing ◽

Overlapping Genes ◽

Genome Sequences ◽

Protein Coding ◽

Coding Regions ◽

Translation Signals ◽

Rats And Mice ◽

Coding Potential ◽

Exon Gene

ABSTRACT Prediction of protein-coding regions and other features of primary DNA sequence have greatly contributed to experimental biology. Significant challenges remain in genome annotation methods, including the identification of small or overlapping genes and the assessment of mRNA splicing or unconventional translation signals in expression. We have employed a combined analysis of compositional biases and conservation together with frame-specific G+C representation to reevaluate and annotate the genome sequences of mouse and rat cytomegaloviruses. Our analysis predicts that there are at least 34 protein-coding regions in these genomes that were not apparent in earlier annotation efforts. These include 17 single-exon genes, three new exons of previously identified genes, a newly identified four-exon gene for a lectin-like protein (in rat cytomegalovirus), and 10 probable frameshift extensions of previously annotated genes. This expanded set of candidate genes provides an additional basis for investigation in cytomegalovirus biology and pathogenesis.

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Evaluation and Fuzzy Classification of Gene Finding Programs on Human Genome Sequences

Fuzzy Systems and Knowledge Discovery - Lecture Notes in Computer Science ◽

10.1007/11540007_102 ◽

2005 ◽

pp. 821-829 ◽

Cited By ~ 2

Author(s):

Atulya Nagar ◽

Sujita Purushothaman ◽

Hissam Tawfik

Keyword(s):

Human Genome ◽

Fuzzy Classification ◽

Gene Finding ◽

Genome Sequences

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A standard variation file format for human genome sequences

Genome Biology ◽

10.1186/gb-2010-11-8-r88 ◽

2010 ◽

Vol 11 (8) ◽

pp. R88 ◽

Cited By ~ 66

Author(s):

Martin G Reese ◽

Barry Moore ◽

Colin Batchelor ◽

Fidel Salas ◽

Fiona Cunningham ◽

...

Keyword(s):

Human Genome ◽

File Format ◽

Genome Sequences

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Generation of small interfering RNA (siRNA) database from SARS-CoV-2 genome sequences

10.21203/rs.3.pex-1207/v1 ◽

2020 ◽

Author(s):

Inácio Gomes Medeiros ◽

André Salim Khayat ◽

Beatriz Stransky ◽

Sidney Emanuel Batista dos Santos ◽

Paulo Pimentel de Assumpção ◽

...

Keyword(s):

Human Genome ◽

Design Process ◽

Small Interfering Rna ◽

Reference Genome ◽

Second Phase ◽

Computational Power ◽

Genome Sequences ◽

Interfering Rna ◽

Reference Genomes

Abstract This protocol aims to describe the building of a database of SARS-CoV-2 targets for siRNA approaches. Starting from the virus reference genome, we will derive sequences from 18 to 21nt-long and verify their similarity against the human genome and coding and non-coding transcriptome, as well as genomes from related viruses. We will also calculate a set of thermodynamic features for those sequences and will infer their efficiencies using three different predictors. The protocol has two main phases: at first, we align sequences against reference genomes. In the second one, we extract the features. The first phase varies in terms of duration, depending on computational power from the running machine and the number of reference genomes. Despite that, the second phase lasts about thirty minutes of execution, also depending on the number of cores of running machine. The constructed database aims to speed the design process by providing a broad set of possible SARS-CoV-2 sequences targets and siRNA sequences.

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IPD-IMGT/HLA Database

Nucleic Acids Research ◽

10.1093/nar/gkz950 ◽

2019 ◽

Cited By ~ 22

Author(s):

James Robinson ◽

Dominic J Barker ◽

Xenia Georgiou ◽

Michael A Cooper ◽

Paul Flicek ◽

...

Keyword(s):

Human Genome ◽

Medical Community ◽

Successful Outcome ◽

Sequence Variants ◽

Polymorphic Region ◽

New Methods ◽

Histocompatibility Complex ◽

The Many ◽

User Friendly ◽

Community Access

Abstract The IPD-IMGT/HLA Database, http://www.ebi.ac.uk/ipd/imgt/hla/, currently contains over 25 000 allele sequence for 45 genes, which are located within the Major Histocompatibility Complex (MHC) of the human genome. This region is the most polymorphic region of the human genome, and the levels of polymorphism seen exceed most other genes. Some of the genes have several thousand variants and are now termed hyperpolymorphic, rather than just simply polymorphic. The IPD-IMGT/HLA Database has provided a stable, highly accessible, user-friendly repository for this information, providing the scientific and medical community access to the many variant sequences of this gene system, that are critical for the successful outcome of transplantation. The number of currently known variants, and dramatic increase in the number of new variants being identified has necessitated a dedicated resource with custom tools for curation and publication. The challenge for the database is to continue to provide a highly curated database of sequence variants, while supporting the increased number of submissions and complexity of sequences. In order to do this, traditional methods of accessing and presenting data will be challenged, and new methods will need to be utilized to keep pace with new discoveries.

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