Answers.Body: <p>To extend a bit more to @gringer answer. RIKEN is a large Japanese research institute, that participates in different scientific collaborations. </p>
  
  <p>One of these is the FANTOM collaboration (Functional ANnotation Of the Mammalian genome), which lately have resulted in the release of <a href="http://fantom.gsc.riken.jp/cat/" rel="nofollow noreferrer">FANTOM CAT</a>, a browsing tool for exploring lncRNA relative to associated Genes, Traits and Ontologies.</p>
  
  <p>Many of the transcripts and genes discovered during this work, are not yet named, and are therefore called CAT-genes, following numbering comparable to ensembl (eg. CATG00000118335.1).</p>
  
  <p>I'm unsure how RIK genes have been discovered, as I have not personally encountered these genes yet, but in case you likewise encounter more genes discovered in collaboration with RIKEN, you now also know of CAT genes.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-20T06:58:20.487Z
Answers.LastActivityDate: 2018-06-21T06:27:39.287Z
Answers.LastEditDate: 2018-06-21T06:27:39.287Z
Answers.UserDisplayName: Kasper Thystrup Karstensen
Answers.Body: <p>My understanding is that these are cDNA sequences from the RIKEN project that don't yet have another gene name. The project carried out a comprehensive sequencing of the mouse genome, and as a result found a lot of cDNA transcripts that were previously unknown. Now they have some annotation (which can be varying degrees of functional annotation), and an accepted official identifier to allow people to talk about these transcripts when discovered in other studies.</p>
  
  <p>It'd be interesting to see if any novel transcripts have been found from the Tabula Muris project. They would also need their own identifier, possibly leading to similar intrigue about their history.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-11T13:53:51.403Z
Answers.Text: cDNA is generated from RNA so they most probably sequenced RNA (the transcriptome) instead of the genome itself.
Answers.UserDisplayName: moritzschaefer
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-03T19:08:28.117Z
Answers.LastActivityDate: 2018-01-03T19:08:28.117Z
Answers.UserDisplayName: gringer
Body: <p>I am using data from the <a href="https://figshare.com/projects/Tabula_Muris_Transcriptomic_characterization_of_20_organs_and_tissues_from_Mus_musculus_at_single_cell_resolution/27733" rel="nofollow noreferrer">Tabula Muris Consortium</a>.</p>
  
  <p>These are gene counts from scRNA-seq of mouse cells.</p>
  
  <p>There are some specific genes with name ending with suffix 'Rik' (e.g. 0610005C13Rik or 0610007C21Rik). Searching online I found that they are from <a href="http://www.sciencedirect.com/science/article/pii/S1631069103002166?via%3Dihub" rel="nofollow noreferrer">RIKEN project</a>.</p>
  
  <p>However, they are different in some respects (e.g. antisense lncRNA gene, or mouse 0610007C21RIK Adenovirus).</p>
  
  <p>I want to exclude them from downstream analysis, but it is unclear to me the main purpose of this collection. For which kind of analysis are they used?</p>
  
Tags: <scrnaseq>
Title: What are RIKEN genes?
ThreadText: # What are RIKEN genes?
  
  (Asked by: username_0 on 2018-01-03)
  
  I am using data from the [Tabula Muris Consortium](https://figshare.com/projects/Tabula_Muris_Transcriptomic_characterization_of_20_organs_and_tissues_from_Mus_musculus_at_single_cell_resolution/27733).
  
  These are gene counts from scRNA-seq of mouse cells.
  
  There are some specific genes with name ending with suffix 'Rik' (e.g. 0610005C13Rik or 0610007C21Rik). Searching online I found that they are from [RIKEN project](http://www.sciencedirect.com/science/article/pii/S1631069103002166?via%3Dihub).
  
  However, they are different in some respects (e.g. antisense lncRNA gene, or mouse 0610007C21RIK Adenovirus).
  
  I want to exclude them from downstream analysis, but it is unclear to me the main purpose of this collection. For which kind of analysis are they used?
  
  **Tags:** scrnaseq
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2018-01-03. Score: 3 | Accepted answer
  
  My understanding is that these are cDNA sequences from the RIKEN project that don't yet have another gene name. The project carried out a comprehensive sequencing of the mouse genome, and as a result found a lot of cDNA transcripts that were previously unknown. Now they have some annotation (which can be varying degrees of functional annotation), and an accepted official identifier to allow people to talk about these transcripts when discovered in other studies.
  
  It'd be interesting to see if any novel transcripts have been found from the Tabula Muris project. They would also need their own identifier, possibly leading to similar intrigue about their history.
  
  > **Comments:**
  > **username_3**: cDNA is generated from RNA so they most probably sequenced RNA (the transcriptome) instead of the genome itself.  
  
  ---
  
  ### Answer by username_1 on 2018-06-20. Score: 2
  
  To extend a bit more to @username_2 answer. RIKEN is a large Japanese research institute, that participates in different scientific collaborations.
  
  One of these is the FANTOM collaboration (Functional ANnotation Of the Mammalian genome), which lately have resulted in the release of [FANTOM CAT](http://fantom.gsc.riken.jp/cat/), a browsing tool for exploring lncRNA relative to associated Genes, Traits and Ontologies.
  
  Many of the transcripts and genes discovered during this work, are not yet named, and are therefore called CAT-genes, following numbering comparable to ensembl (eg. CATG00000118335.1).
  
  I'm unsure how RIK genes have been discovered, as I have not personally encountered these genes yet, but in case you likewise encounter more genes discovered in collaboration with RIKEN, you now also know of CAT genes.
  
  
  ---
  
  