ArticleBMC genomics2007
Mapping of transcription start sites of human retina expressed genes.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 16 citations in OpenAlex.
- Retinal prolactin isoform PRLΔE1 sustains rod disease in inherited retinal degenerations.Cell death & disease · 2024Article
- Polyglutamine-expanded ATXN7 alters a specific epigenetic signature underlying photoreceptor identity gene expression in SCA7 mouse retinopathy.Journal of biomedical science · 2022Article
- Investigation of promoter regions, motifs, and CpG islands in the regulation of gene expression in Trametes hirsuta strain 072.Journal, genetic engineering & biotechnology · 2021Article
- Where does transcription start? 5'-RACE adapted to next-generation sequencing.Nucleic acids research · 2016Article
- Melanocortin 3 receptor has a 5' exon that directs translation of apically localized protein from the second in-frame ATG.Molecular endocrinology (Baltimore, Md.) · 2014Article
- Isoform diversity and its importance for axon regeneration.Neuropathology : official journal of the Japanese Society of Neuropathology · 2012Review
- Mitotic recombination of chromosome arm 17q as a cause of loss of heterozygosity of NF1 in neurofibromatosis type 1-associated glomus tumors.Genes, chromosomes & cancer · 2012Article
- Variation in the IGF2 gene promoter region is associated with intramuscular fat content in porcine skeletal muscle.Molecular biology reports · 2012Article
- Regulatory polymorphisms in the bovine Ankyrin 1 gene promoter are associated with tenderness and intramuscular fat content.BMC genetics · 2010Article
- Mapping of the transcription start site (TSS) and identification of SNPs in the bovine neuropeptide Y (NPY) gene.BMC genetics · 2008Article
- Bioinformatic identification of novel putative photoreceptor specific cis-elements.BMC bioinformatics · 2007Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe proper assembly of the transcriptional initiation machinery is a key regulatory step in the execution of the correct program of mRNA synthesis. The use of alternative transcription start sites (TSSs) provides a mechanism for cell and tissue specific gene regulation. Our knowledge of transcriptional initiation sequences in the human genome is limited despite the availability of the complete genome sequence. While genome wide experimental and bioinformatic approaches are improving our knowledge of TSSs, they lack information concerning genes expressed in a restricted manner or at very low levels, such as tissue specific genes.
resultsIn this study we describe the mapping of TSSs of genes expressed in human retina. Genes have been selected on the basis of their physiological or developmental role in this tissue. Our work combines in silico analysis of ESTs and known algorithm predictions together with their experimental validation via Cap-finder RACE. We report here the TSSs mapping of 54 retina expressed genes: we retrieved new sequences for 41 genes, some of which contain un-annotated exons. Results can be grouped into five categories, compared to the RefSeq; (i) TSS located in new first exons, (ii) splicing variation of the second exon, (iii) extension of the annotated first exon, (iv) shortening of the annotated first exon, (v) confirmation of previously annotated TSS.
conclusionIn silico and experimental analysis of the transcripts proved to be essential for the ultimate mapping of TSSs. Our results highlight the necessity of a tissue specific approach to complete the existing gene annotation. The new TSSs and transcribed sequences are essential for further exploration of the promoter and other cis-regulatory sequences at the 5'end of genes.
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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.