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I'm trying to wrap my head around the diversity of functions in a genome. Obviously, you've got coding and non-coding regions. But within "non-coding" regions, it seems to be a "wild west" to me. Transposable elements, SINEs, LINEs, transposons, retrotransposons, introns, promotors, etc. Have we annotated genomes enough to have a comprehensive list of the types of non-coding sequences?

It'd be really helpful for me to have a list of the types of non-coding sequences and sub-categories (where relevant). Wikipedia seems to break out a list but the figure on the same page for the human genome doesn't match. Can anyone provide a good reference for how to categorize non-coding sequences?

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  • $\begingroup$ Is this the Wikipedia article, you are referring to? Which figure is the one that doesn't match? $\endgroup$ – Arsak Jul 27 '18 at 14:09
  • $\begingroup$ No, I was referring to "Genome" en.wikipedia.org/wiki/Genome#Eukaryotic_genomes but I had just found this page which is helpful. Thanks. $\endgroup$ – CephBirk Jul 27 '18 at 16:28
  • $\begingroup$ thanks for adding. However, I think the figure and text do align. The text says Noncoding sequences make up 98% of the human genome and the figure says that 2% are Protein-coding genes. Everything else is non-coding :) $\endgroup$ – Arsak Jul 27 '18 at 17:04
  • $\begingroup$ Check out the Sequence Ontology, for one approach to categorizing sequence features. Alternatively, you could download a GFF3 file for the hg38 assembly of the human genome (for example from the ENSEMBL website. One of the columns in that file contains feature types. $\endgroup$ – mdperry Jul 27 '18 at 23:15
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Here's my likely over-simplified and incomplete categorization I could come up with. Please, for those more informed, please edit!

Noncoding sequences can be broken up into the following categories:

1. RNA genes (genes that produce tRNAs, rRNAs, miRNAs, etc.)
2. Introns and untranslated regions (UTRs)
3. Cis- and trans-regulatory elements
    3.1. Cis-regulatory elements (CREs)
        3.1.1. Promoters
        3.1.2. Enhancers
        3.1.3. Silencers
    3.2. Trans-regulatory elements (genes for transcription factors)
4. Repetitive elements (repeated sequences, repeats)
    4.1. Long terminal repeats (LTRs)
    4.2. Variable number tandem repeats (VNTRs, tandem repeats)
        4.2.1. Satellites
        4.2.2. Minisatellites
        4.2.3. Microsatellites (short tandem repeats, simple sequence repeats)
    4.3 Transposable elements (TEs, transposons)
        4.3.1. Retrotransposons (Class I TEs)
            4.3.1.1. Short interspersed nuclear elements (SINEs)
            4.3.1.2. Long interspersed nuclear elements (LINEs)
        4.3.2. DNA transposons (Class II TEs)
    4.4. Telomeres
5. Pseudogenes
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