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While annotations between RefSeq and Gencode are not so different is the coding regions (genes), Gencode is much more rich in the intergenic regions. This could be very advantagous for epigenetic studies, where regulation is of interest. Officially, the Ensembl and GENCODE gene models are the same.

GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project. The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-coding genes within the ENCODE regions (approx. 1% of Human genome).

Officially, the Ensembl and GENCODE gene models are the same. On the latest human and mouse genome assemblies (hg38 and mm10), the identifiers, transcript sequences, and exon coordinates are almost identical between equivalent Ensembl and GENCODE versions (excluding alternative sequences or fix sequences).

DNA transcription is the process by which the genetic information contained within DNA is re-written into messenger RNA (mRNA) by RNA polymerase. This mRNA then exits the nucleus, where it acts as the basis for the translation of DNA.

Transcription is the process in which a gene's DNA sequence is copied (transcribed) to make an RNA molecule. RNA polymerase is the main transcription enzyme. Transcription begins when RNA polymerase binds to a promoter sequence near the beginning of a gene (directly or through helper proteins).

A gene is a unit of the genome stored in the form of DNA. It can be transcribed into mRNA (the transcript) to be used as a template in protein synthesis. A gene can come in many different versions unique to an individual.

There are average 3.42 transcripts per gene. In this study, we did not attempt to discover novel alternatively spliced mRNA isoforms and we relied on the transcript annotations released by GTEx (based on GENCODE version 26).