The Matched Annotation from NCBI and EMBL-EBI (MANE) project aims to produce a matched set of
high-confidence transcripts that are identically annotated between RefSeq (NCBI) and
Ensembl/GENCODE (led by EMBL-EBI). Transcripts for MANE are chosen by a combination of
automated and manual methods based on conservation, expression levels, clinical significance,
and other factors. Transcripts are matched between the NCBI RefSeq and Ensembl/GENCODE annotations
based on the GRCh38 genome assembly, with precise 5’ and 3’ ends defined by high-throughput
sequencing or other available data.
Note that MANE v0.6 (July 2019) is a beta release and only covers 57% of protein coding genes.
RefSeq and Ensembl will continue to develop this single transcript gene set and provide
comprehensive sets of alternate transcripts in the RefSeq-All and the GENCODE tracks.
The raw data can be explored interactively with the Table Browser, or the Data Integrator. For computational analysis, genome annotations are stored in
a bigGenePred file that can be downloaded from the
server. Regional or genome-wide annotations can be converted from binary data to human readable
text using our command line utility bigBedToBed which can be compiled from source code or
downloaded as a precompiled binary for your system. Files and instructions can be found in the
The utility can be used to obtain features within a given range, for example:
bigBedToBed -chrom=chr6 -start=0 -end=1000000 http://hgdownload.soe.ucsc.edu/gbdb/hg38/mane/mane.0.6.bb stdout
Please refer to our Data Access FAQ
for more information or our mailing list for archived user questions.
Thank you to the RefSeq project at NCBI and the Ensembl/GENCODE project at EMBL-EBI.
You can contact the authors directly at
Download links for MANE Select v0.6: ftp://ftp.ncbi.nlm.nih.gov/refseq/MANE