MANE v1.0 Track Settings
 
NCBI RefSeq and Ensembl transcripts from the MANE Project (v1.0)   (All Genes and Gene Predictions tracks)

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Label: Gene symbol    Ensembl id    Ensembl protein identifier, none for noncoding    Ensembl Gene identifier    NCBI id    NCBI protein identifier, none for noncoding    NCBI gene   

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Data last updated at UCSC: 2022-02-12 22:01:54

Description

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.

The current release (MANE v1.0) includes coverage of 99% of human protein-coding genes and 99.8% of genes of clinical relevance, including genes in the American College of Medical Genetics and Genomics (ACMG) Secondary Findings list (SF) v3.0. This release includes both MANE Select (19062) and MANE Plus Clinical (58) transcripts. MANE Plus Clinical items are colored red.

For more information on the different gene tracks, including MANE vs GENCODE or RefSeq, see our Genes FAQ.

Data Access

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 download 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 utilities directory. 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.1.0.bb stdout

Download links for MANE Select v1.0: ftp://ftp.ncbi.nlm.nih.gov/refseq/MANE

Please refer to our Data Access FAQ for more information or our mailing list for archived user questions.

Credits

Thank you to the RefSeq project at NCBI and the Ensembl/GENCODE project at EMBL-EBI. You can contact the authors directly at MANE-help@ncbi.nlm.nih.gov or mane-help@ebi.ac.uk.

References

Morales J, Pujar S, Loveland JE, Astashyn A, Bennett R, Berry A, Cox E, Davidson C, Ermolaeva O, Farrell CM et al. A joint NCBI and EMBL-EBI transcript set for clinical genomics and research. Nature. 2022 Apr;604(7905):310-315. PMID: 35388217; PMC: PMC9007741