SinEx DB: a database for single exon coding sequences in mammalian genomes

Abstract

Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as ‘single exon genes’ (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl

The Reprimo Gene Family: A Novel Gene Lineage in Gastric Cancer with Tumor Suppressive Properties

“…Originally described as a p53-dependent cell cycle arrest mediator ( Figure 4 ), yet the functions and mechanisms by which RPRM acts still remain unknown. Evolutionary studies, developmental genetics and molecular biology approaches will prove useful tools in determining the origin and function of this single exon and intronless RPRM gene family [ 7 , 66 ]. The evaluation of different and complementary lines of evidence such as (1) selective pressures; (2) phenotypical variations as a consequence of loss- or gain-of-function; and (3) pre- and post-transcriptional and translational variations may deliver a better understanding of this gene family.…”

Improved ontology for eukaryotic single-exon coding sequences in biological databases

“…The estimated proportion of uiSEGs, IGs and SEIs within the human genome is about 2:1:1 and the latter group could have caused bias in earlier studies of SEG function and evolution in the human genome ( 5 , 8 , 14–17 , 43 ). The unambiguous identification of SEIs also provides opportunities to study novel aspects of alternative splicing and intron evolution, gene evolution, RNA editing, nuclear export pathways and transcriptional regulation.…”

“…Eukaryotic genes are usually interrupted by intragenic, non-protein coding regions termed introns that are removed by RNA splicing during maturation of the final RNA product. However, more than 2000 protein-coding genes in human genome have been shown to lack introns and have been termed SEGs, defined as a nuclear, protein-coding gene that lack introns in their CDSs ( 5 ). This definition excludes genes that generate functional RNAs such as tRNA, rRNA and long non-coding RNAs.…”

“…Examples of uiSEGs with experimentally validatedphenotypes of clinical relevance are as follows: ERAS, embryonic stem cell expressed Ras; NEUROD2, neuronal differentiation 2; and NFIL3, nuclear factor, interleukin-3-regulated protein ( 5 , 11 , 12 ).…”

“…Today, most genes are predicted based mainly on bioinformatics analyses. Inparticular, SEGs are identified based on CDS (protein coding) gene identifiers in annotated genomes ( 5 , 14–16 ) and these identifiers do not include information from the UTR of genes, resulting in the identification of all SEGs as IGs, regardless of the presence or absence of introns in their UTRs ( 14–18 ) with the result that the terms ‘SEG’ and ‘IG’ are rife with ambiguity.…”