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Critical evaluation...
Critical evaluation of the FANTOM3 non-coding RNA transcripts
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- Nordström, Karl J V (author)
- Uppsala universitet,Funktionell farmakologi
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- Mirza, Majd A I (author)
- Uppsala universitet,Funktionell farmakologi
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- Almén, Markus Sällman (author)
- Uppsala universitet,Funktionell farmakologi
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- Gloriam, David E (author)
- Uppsala universitet,Funktionell farmakologi
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- Fredriksson, Robert (author)
- Uppsala universitet,Funktionell farmakologi
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- Schiöth, Helgi B (author)
- Uppsala universitet,Funktionell farmakologi
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(creator_code:org_t)
- Elsevier BV, 2009
- 2009
- English.
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In: Genomics. - : Elsevier BV. - 0888-7543 .- 1089-8646. ; 94:3, s. 169-176
- Related links:
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https://doi.org/10.1...
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https://urn.kb.se/re...
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Abstract
Subject headings
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- We studied the genomic positions of 38,129 putative ncRNAs from the RIKEN dataset in relation to protein-coding genes. We found that the dataset has 41% sense, 6% antisense, 24% intronic and 29% intergenic transcripts. Interestingly, 17,678 (47%) of the FANTOM3 transcripts were found to potentially be internally primed from longer transcripts. The highest fraction of these transcripts was found among the intronic transcripts and as many as 77% or 6929 intronic transcripts were both internally primed and unspliced. We defined a filtered subset of 8535 transcripts that did not overlap with protein-coding genes, did not contain ORFs longer than 100 residues and were not internally primed. This dataset contains 53% of the FANTOM3 transcripts associated to known ncRNA in RNAdb and expands previous similar efforts with 6523 novel transcripts. This bioinformatic filtering of the FANTOM3 non-coding dataset has generated a lead dataset of transcripts without signs of being artefacts, providing a suitable dataset for investigation with hybridization-based techniques.
Keyword
- RIKEN
- FANTOM3
- ncRNA
- Non-coding RNA
- snoRNA
- EST
- MEDICINE
- MEDICIN
Publication and Content Type
- ref (subject category)
- art (subject category)
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