ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2015
Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
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Who cites it
27 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic reanalysis of partial trisomy 21 cases with or without Down syndrome suggests a small region on 21q22.13 as critical to the phenotype.Human molecular genetics · 2016Pooled it
- The shortest animal introns: insights from parasitic cnidarians.Molecular biology and evolution · 2026Article
- Minigenes enhance heterologous expression and prevent aberrant splicing of mouse Spink1.Scientific reports · 2025Article
- Distribution of estrogen sulfotransferase genes in tunas and their relatives.BMC research notes · 2025Article
- Improving the RNA velocity approach with single-cell RNA lifecycle (nascent, mature and degrading RNAs) sequencing technologies.Nucleic acids research · 2023Article
- Introns: the "dark matter" of the eukaryotic genome.Frontiers in genetics · 2023Review
- The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns.Open biology · 2022Article
- LncRNAs Are Differentially Expressed between Wildtype and Cell Line Strains of African Trypanosomes.Non-coding RNA · 2022Article
- SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency.BMC bioinformatics · 2021Article
- The transcriptome profile of human trisomy 21 blood cells.Human genomics · 2021Article
- Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes.BMC bioinformatics · 2020Article
- Genetics of Gene Expression in the Aging Human Brain Reveal TDP-43 Proteinopathy Pathophysiology.Neuron · 2020Article
- Article
- Partial trisomy 21 map: Ten cases further supporting the highly restricted Down syndrome critical region (HR-DSCR) on human chromosome 21.Molecular genetics & genomic medicine · 2019Article
- Reference quantitative transcriptome dataset for adultData in brief · 2019Article
- Human protein-coding genes and gene feature statistics in 2019.BMC research notes · 2019Article
- Dataset of differential gene expression between total normal human thyroid and histologically normal thyroid adjacent to papillary thyroid carcinoma.Data in brief · 2019Article
- On the length, weight and GC content of the human genome.BMC research notes · 2019Article
- Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within "Nassophorea-Synhymenia-Phyllopharyngea" Assemblage.Frontiers in microbiology · 2019Article
- Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes.BMC genomics · 2018Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have developed GeneBase, a full parser of the National Center for Biotechnology Information (NCBI) Gene database, which generates a fully structured local database with an intuitive user-friendly graphic interface for personal computers. Features of all the annotated eukaryotic genes are accessible through three main software tables, including for each entry details such as the gene summary, the gene exon/intron structure and the specific Gene Ontology attributions. The structuring of the data, the creation of additional calculation fields and the integration with nucleotide sequences allow users to make many types of comparisons and calculations that are useful for data retrieval and analysis. We provide an original example analysis of the existing introns across all the available species, through which the classic biological problem of the 'minimal intron' may find a solution using available data. Based on all currently available data, we can define the shortest known eukaryotic GT-AG intron length, setting the physical limit at the 30 base pair intron belonging to the human MST1L gene. This 'model intron' will shed light on the minimal requirement elements of recognition used for conventional splicing functioning. Remarkably, this size is indeed consistent with the sum of the splicing consensus sequence lengths.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.