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Discrepancy in gene counts between GENCODE 23 and Ensembl 81/82?

I see the GENCODE 23 general statistics shows total number of protein-coding genes as 19797 in humans http://www.gencodegenes.org/stats/current.html, whereas Ensembl 81 contains 22017 unique protein-coding genes when I use filter for "protein_coding" Gene type (biotype) and "GENCODE basic annotation" using Ensembl BioMart services http://www.ensembl.org/biomart/martview/034b08dbbcea12ff30614193d4d293a0. As I understand ensembl imports the GENCODE gene-set and annotations, the gene counts should correlate. Could anyone please explain me what I am missing and why is this difference in the gene counts?

Thanks!

gene gencode biomart ensembl genome
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updated by Ram Ram • written by Veerendra Gadekar • Veerendra Gadekar

We don't import Gencode, we make Gencode.

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written by Emily Emily

I'm not sure who deleted this post, but I've undeleted it.

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written by Devon Ryan Devon Ryan

1 answer

22017 is the number of protein coding genes you get if you include patches, scaffolds and alternate haplotype contigs. If you exclude those, you'll get 19779 (the difference of 18 is due to Gencode including annotations for genes on the pseudoautosomal region of chrY).

There are multiple "basic" annotations from Gencode, one contains only the 25 regular chromosomes and has 19797 protein coding genes, the other has ~22000 protein coding genes, due to containing alternate haplotypes and patches and scaffolds.

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written by Devon Ryan Devon Ryan

I got these from the GTF files (for release 82) that were used to generate the numbers on the webpages you're seeing. The 20296 presumably comes from adding in the ~500 "read through" genes (there's still a difference of 4 that are presumably from something else). I'm just getting these numbers with grep and awk, btw.

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written by Devon Ryan Devon Ryan

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