Matched Annotation from NCBI and EMBL-EBI (MANE)

This track hub contains transcripts from the Matched Annotation from NCBI and EMBL-EBI (MANE) Project.

MANE was originally planned as a collaborative project that aims to converge on human protein-coding gene and transcript annotation for a genome wide set of representative transcripts and corresponding proteins (when applicable). Each MANE transcript represents an exact match in exon coordinates, coding region, and sequence between a Refseq transcript and its counterpart in the Ensembl/GENCODE annotation such that the two identifiers can be used synonymously. Further, a MANE transcript matches GRCh38 reference genome assembly perfectly and is chosen based on biologically relevant criteria such as transcript expression levels and conservation of coding regions. In the last two years, clinically relevant non-coding genes have been added to MANE based on reports in literature and feedback from collaborating groups. Currently, the following products are provided in MANE datasets:

  1. MANE Select: The MANE Select set consists of one transcript at each locus across the genome that is representative of biology at that locus, including protein-coding genes and a targeted subset of non-coding genes. This set is useful as a universal standard for clinical reporting, as a default for display on browsers and key genomic resources, and as a starting point for comparative genomics or functional studies. MANE Select transcripts are identified using computational methods complemented by manual review and discussion.
  2. MANE Plus Clinical: The MANE Plus Clinical set includes additional transcripts for genes where MANE Select alone is not sufficient to report all "Pathogenic (P)" or "Likely Pathogenic (LP)" clinical variants available in public resources.

Watch the MANE webinar on YouTube!

Track Display Conventions and Configuration

Releases up to version 0.9 contain a single track containing two identical transcripts for each gene, colored as follows:

  1. MANE Select transcript using NCBI identifiers
  2. MANE Select transcript using EMBL-EBI identifiers

Starting with version 0.91, two tracks are provided - one each with NCBI and EMBL-EBI identifiers.

  1. By default, only the transcript identifier is shown in the label. This can be changed to combinations of transcript, protein and gene identifiers.
  2. Transcripts within each track are colored as follows:
    1. MANE Select transcript
    2. MANE Plus Clinical transcript
  3. By default, both MANE Select and MANE Plus Clinical transcripts are displayed. But the tracks can be filtered to show only one type of transcripts.

Data Access

MANE data can be downloaded from the NCBI FTP site. Separate files are provided in GFF3, GTF, BigBed and FASTA formats for both the RefSeq and Ensembl identifiers, and additionally in GenBank flatfile format for the RefSeq transcripts and proteins.

Citing MANE

Please use the following publication to cite MANE:
Morales, J., Pujar, S., Loveland, J.E. et al. A joint NCBI and EMBL-EBI transcript set for clinical genomics and research. Nature. 2022 Apr;604(7905):310-315.
PubMed; PubMed Central; DOI: 10.1038/s41586-022-04558-8

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