# Does the BrainSpan RNA-Seq data cover only protein-coding genes?
**URL:** https://community.brain-map.org/t/does-the-brainspan-rna-seq-data-cover-only-protein-coding-genes/1345
**Category:** General
**Tags:** atlas-human-brain-developing, transcriptomics, rna-seq
**Created:** [November 15, 2021, 5:31am UTC](https://community.brain-map.org/t/does-the-brainspan-rna-seq-data-cover-only-protein-coding-genes/1345 "2021-11-15T05:31:20Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@miro](https://community.brain-map.org/u/miro)
#### Post date: [November 15, 2021, 5:31am UTC](https://community.brain-map.org/t/does-the-brainspan-rna-seq-data-cover-only-protein-coding-genes/1345/1 "2021-11-15T05:31:20Z")
Hello,
I am analysing the RNA-Seq data from the BrainSpan Atlas of the Developing Human Brain. I have seen that this dataset contains RNA-Seq RPKM values for 52376 genes.
I have read the [documentation](https://www.brainspan.org/static/download.html) on how the RNA was extracted from the brain tissues, and there is a section called ‘mRNA Library Preparation and Sequencing’ which states that mRNA was purified from the total RNA. I have also read that the Gencode gene annotations were used in the alignment of the reads to the reference genome.
If only mRNA was sequenced, why does the BrainSpan RNA-Seq dataset have RPKM values for 52376 genes? There are ~20,000 protein coding genes, and the most [recent](https://www.gencodegenes.org/human/stats.html) Gencode release has annotations for 19955 protein coding genes.
Thanks.
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### Author:  [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)
#### Post date: [November 15, 2021, 3:52pm UTC](https://community.brain-map.org/t/does-the-brainspan-rna-seq-data-cover-only-protein-coding-genes/1345/2 "2021-11-15T15:52:32Z")
All transcripts available from Genecode v10 are included in alignment for RNA-seq data (which can be downloaded [here](http://www.brainspan.org/static/download.html)). This includes protein coding genes, as well as non-coding transcripts (e.g., lincRNAs) and pseudogenes. Inclusion does not necessarily mean that there is expression in the brain; however, we do find that some are expressed, and quite a few show cell type specificity in the [Allen Cell Types Database](https://portal.brain-map.org/atlases-and-data/rnaseq).