ArticleBMC genomics2013
Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers, 1 of them a synthesis that pooled it.
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Who cites it
124 citing papers in PubMed, 1 synthesis or guideline pooled it, 171 citations in OpenAlex.
- Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data.BMC genomics · 2023Pooled it
- Alternative splicing governs cone cyclic nucleotide-gated (CNG) channel sensitivity to regulation by phosphoinositides.The Journal of biological chemistry · 2014Trial
- Revisiting retinal and macular degeneration in the genomics era.Nature reviews. Genetics · 2026Review
- Paired DNA and RNA sequencing uncovers common and rare variation regulating human retinal gene expression.Nature communications · 2026Article
- Restoring Sight: The Journey of AIPL1 from Discovery to Therapy.International journal of molecular sciences · 2025Review
- RNA dysfunction in age-related macular degeneration: the role of U1 snRNP complex and neurodegenerative diseases.International journal of retina and vitreous · 2025Review
- Article
- Identifying X-chromosome variants associated with age-related macular degeneration.Human molecular genetics · 2024Article
- Autosomal-dominant macular dystrophy linked to a chromosome 17 tandem duplication.JCI insight · 2024Article
- Coding and non-coding variants in the ciliopathy gene CFAP410 cause early-onset non-syndromic retinal degeneration.NPJ genomic medicine · 2024Article
- Antisense Oligonucleotide STK-002 Increases OPA1 in Retina and Improves Mitochondrial Function in Autosomal Dominant Optic Atrophy Cells.Nucleic acid therapeutics · 2024Article
- Differential gene expression between central and peripheral retinal regions in dogs and comparison with humans.Experimental eye research · 2024Article
- Genome wide association study and genomic risk prediction of age related macular degeneration in Israel.Scientific reports · 2024Article
- Precision ophthalmology: a call for Africa not to be left in the dark.Gene therapy · 2024Article
- A proteogenomic atlas of the human neural retina.Frontiers in genetics · 2024Article
- The splicing factor DHX38 enables retinal development through safeguarding genome integrity.iScience · 2023Article
- Alternative RNA Splicing in the Retina: Insights and Perspectives.Cold Spring Harbor perspectives in medicine · 2023Review
- A 69 kb Deletion in chr19q13.42 includingJournal of clinical medicine · 2022Article
- Likely pathogenic structural variants in genetically unsolved patients with retinitis pigmentosa revealed by long-read sequencing.Journal of medical genetics · 2022Article
- Noncanonical Splice Site and Deep Intronic FRMD7 Variants Activate Cryptic Exons in X-linked Infantile Nystagmus.Translational vision science & technology · 2022Article
64 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundThe retina is a complex tissue comprised of multiple cell types that is affected by a diverse set of diseases that are important causes of vision loss. Characterizing the transcripts, both annotated and novel, that are expressed in a given tissue has become vital for understanding the mechanisms underlying the pathology of disease.
resultsWe sequenced RNA prepared from three normal human retinas and characterized the retinal transcriptome at an unprecedented level due to the increased depth of sampling provided by the RNA-seq approach. We used a non-redundant reference transcriptome from all of the empirically-determined human reference tracks to identify annotated and novel sequences expressed in the retina. We detected 79,915 novel alternative splicing events, including 29,887 novel exons, 21,757 3' and 5' alternate splice sites, and 28,271 exon skipping events. We also identified 116 potential novel genes. These data represent a significant addition to the annotated human transcriptome. For example, the novel exons detected increase the number of identified exons by 3%. Using a high-throughput RNA capture approach to validate 14,696 of these novel transcriptome features we found that 99% of the putative novel events can be reproducibly detected. Further, 15-36% of the novel splicing events maintain an open reading frame, suggesting they produce novel protein products.
conclusionsTo our knowledge, this is the first application of RNA capture to perform large-scale validation of novel transcriptome features. In total, these analyses provide extensive detail about a previously uncharacterized level of transcript diversity in the human retina.
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Registered trials
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.