GenCode has a wonderful breakdown of the number of coding/non-coding genes and transcripts here...

http://www.gencodegenes.org/stats.html

Does a similar breakdown exist for RefSeq anywhere?  Thanks!
I don't believe RefSeq do as good a breakdown of transcript types as GENCODE, however, you may be interested in the following resources:

 - <a
   href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-16-S8-S2">Comparison
   of GENCODE and RefSeq gene annotation and the impact of reference
   geneset on variant effect prediction</a>
 - <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245008/">NCBI
   Reference Sequences (RefSeq): current status, new features and genome
   annotation policy</a>
 - <a
   href="https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1308-8">A
   comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in
   the context of RNA-seq read mapping and gene quantification</a>

Generally, I think that you'll find that GENCODE is more comprehensive for non-coding genes; however, for the majority of these, exact function is entirely unknown. Most people filter them out of, for example, RNA-seq experiments, in order to (in part) minimise the stringency of a false discovery rate threshold. On the other hand, RefSeq has the feel of a well-curated resource.

Kevin

