There are many other tracks in the group "Genes and Gene Predictions". Genscan and N-Scan are older transcript predictor algorithms that are based on the genome sequence alone. Augustus and AceView are automated gene-predictors that use cDNA and EST data. These and similar gene tracks are only relevant when you are working on a particular locus where you think that the manually curated gene models (Ensembl and RefSeq) have errors.
++To illustrate differences between the most common gene tracks, here is an +overview of a few different tracks on human (hg38) and how many transcripts +they contain as of March 2019: +
+ +| Track name | +Number of transcripts | +
|---|---|
| Known Gene (Gencode comprehensive V29) | +226,811 | +
| Known Gene (Gencode basic V29) | +112,634 | +
| NCBI RefSeq Predicted Transcripts | +94,389 | +
| UCSC RefSeq (Curated) | +80,694 | +
| NCBI RefSeq Curated | +73,080 | +
| CCDS | +32,506 | +
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).
GENCODE uses the UCSC convention of prefixing chromosome names with "chr", e.g.