The next release (v1.4) of Matched Annotation from NCBI and EMBL-EBI (MANE) is here! MANE is a collaborative dataset produced jointly by NCBI and EMBL-EBI that provides a representative transcript (MANE Select) for human protein-coding genes, to be used as universal standards for variant reporting and browser display. A second transcript, MANE Plus Clinical, is provided for genes where MANE Select alone is not sufficient to report all known variants. The new MANE release adds another important component to this high-value dataset – non-coding genes, some of which are known to be associated with human disease.
What’s new?
This release, built from RefSeq Annotation GCF_000001405.40-RS_2024_08 and Ensembl release 114, contains 19,338 MANE Select and 66 MANE Plus Clinical transcripts. It also includes the first batch of fifty non-coding genes that are associated with human disease, chosen based on publications and input from collaborating groups.
- For example, this set includes the small nuclear RNA gene RNU4ATAC, implicated in RNU4ATAC Spectrum Disorder, and the long noncoding RNA (lncRNA) gene MALAT1, reported as a therapeutic target in several types of cancer, including breast cancer.
A new data file included on the FTP site provides information about genes where the original MANE Select was updated. The MANE set is intended to be stable, however rare updates are made in response to issues flagged by quality assurance tests, new published data, or external datasets. Look for the list in this file: MANE.GRCh38.v1.4.changed_select_accessions.txt.gz.
- For example, the decision to switch MANE Select transcript for IL36B (GeneID: 27177) from NM_014438.5 (ENST00000259213.9) to NM_173178.3 (ENST00000327407.2) was informed by the higher per-residue model confidence score (pLDDT score) of the AlphaFold prediction for NM_173178.3. This is one of the eight MANE Select switches made based on the analysis in Sommer et al., 2022.
Figure: Genome Data Viewer displaying the lncRNA gene MALAT1 (NCBI GeneID:378938) with the MANE v1.4 track (top) showing the MANE Select NR_002819.5 and all transcripts included in RefSeq Annotation GCF_000001405.40-RS_2024_08 (bottom).
Access the Data
- Download the MANE dataset
- View MANE Select records in the Nucleotide or Protein databases
- Interactively explore MANE sequence data in the Genome Data Viewer
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