Schema for MANE v1.0 - NCBI RefSeq and Ensembl transcripts from the MANE Project (v1.0)
  Database: hg38    Primary Table: mane Data last updated: 2022-02-12
Big Bed File: /gbdb/hg38/mane/mane.1.0.bb
Item Count: 19,120
Format description: MANE bigGenePred
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart166069298Start position in chromosome
chromEnd166167001End position in chromosome
nameENST00000354422.4Ensembl id
score0Score (0-1000)
strand-+ or - for strand
thickStart166070240Start of where display should be thick (start codon)
thickEnd166166248End of where display should be thick (stop codon)
reserved8,81,156RGB value (use R,G,B string in input file)
blockCount2Number of blocks
blockSizes1465,1016,Comma separated list of block sizes
chromStarts0,96687,Start positions relative to chromStart
name2ENST00000354422.4Alternative/human readable name
cdsStartStatcmplStatus of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStatcmplStatus of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames2,0,Exon frame {0,1,2}, or -1 if no frame for exon
typemRNATranscript type
geneNameENSG00000188859.7Ensembl Gene identifier
geneName2FAM78BGene symbol
geneTypeprotein_codingGene type
ensemblProtAccENSP00000346404.3Ensembl protein identifier, none for noncoding
ncbiIdNM_001017961.5NCBI id
ncbiGeneGeneID:149297NCBI gene
ncbiProtAccNP_001017961.1NCBI protein identifier, none for noncoding
maneStatMANE SelectMANE transcript status

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsname2cdsStartStatcdsEndStatexonFramestypegeneNamegeneName2geneTypeensemblProtAccncbiIdncbiGenencbiProtAccmaneStat
chr1166069298166167001ENST00000354422.40-1660702401661662488,81,15621465,1016,0,96687,ENST00000354422.4cmplcmpl2,0,mRNAENSG00000188859.7FAM78Bprotein_codingENSP00000346404.3NM_001017961.5GeneID:149297NP_001017961.1MANE Select
chr1166839474166856359ENST00000367876.90+1668409561668504098,81,1566130,134,127,99,1486,3775,0,1480,7137,8019,9463,13110,ENST00000367876.9cmplcmpl-1,0,0,1,1,-1,mRNAENSG00000143157.12POGKprotein_codingENSP00000356850.4NM_017542.5GeneID:57645NP_060012.3MANE Select
chr1166856509166876264ENST00000367874.50-1668575661668762338,81,15681210,163,152,210,98,66,92,105,0,1609,3676,5693,7314,12935,13253,19650,ENST00000367874.5cmplcmpl0,2,0,0,1,1,2,0,mRNAENSG00000152382.6TADA1protein_codingENSP00000356848.4NM_053053.4GeneID:117143NP_444281.1MANE Select
chr1166908186166975540ENST00000271417.80-1669193541669752688,81,1561011204,673,217,114,177,147,57,120,333,318,0,12520,14406,18880,27114,28404,31327,48546,49582,67036,ENST00000271417.8cmplcmpl0,2,1,1,1,1,1,1,1,0,mRNAENSG00000143195.13ILDR2protein_codingENSP00000271417.2NM_199351.3GeneID:387597NP_955383.1MANE Select
chr1166989279167022214ENST00000367872.90+1669893521670218558,81,15612205,93,100,156,42,125,55,142,63,133,76,547,0,457,2098,3406,4748,14900,15796,15976,26942,28547,31805,32388,ENST00000367872.9cmplcmpl0,0,0,1,1,1,0,1,2,2,0,1,mRNAENSG00000143194.13MAELprotein_codingENSP00000356846.4NM_032858.3GeneID:84944NP_116247.1MANE Select
chr1167052835167090377ENST00000367868.40-1670543331670902878,81,15671631,136,120,156,217,155,133,0,2140,2894,10746,16086,20549,37409,ENST00000367868.4cmplcmpl2,1,1,1,0,1,0,mRNAENSG00000143167.12GPA33protein_codingENSP00000356842.3NM_005814.3GeneID:10223NP_005805.1MANE Select
chr1167094074167129165ENST00000361200.70+1670948491671286088,81,1566120,126,95,232,218,3379,0,759,19635,23253,25174,31712,ENST00000361200.7cmplcmpl-1,0,2,1,2,1,mRNAENSG00000198842.10STYXL2protein_codingENSP00000354483.2NM_001080426.3GeneID:92235NP_001073895.1MANE Select
chr1167220885167427340ENST00000367866.70+1672208971674158108,81,1561673,66,101,54,120,189,127,95,174,142,140,180,106,346,89,11841,0,111584,144581,149275,151031,153222,155143,162971,168702,175400,177108,178300,180565,191073,192140,194614,ENST00000367866.7cmplcmpl0,1,1,0,0,0,0,1,0,0,1,0,0,1,2,1,mRNAENSG00000143190.23POU2F1protein_codingENSP00000356840.2NM_002697.4GeneID:5451NP_002688.3MANE Select
chr1167430639167518529ENST00000362089.100-1674316801675184658,81,15681107,36,57,36,81,57,104,122,0,2384,3380,4759,7930,8704,10024,87768,ENST00000362089.10cmplcmpl0,0,0,0,0,0,1,0,mRNAENSG00000198821.12CD247protein_codingENSP00000354782.5NM_198053.3GeneID:919NP_932170.1MANE Select
chr1167541012167553762ENST00000370509.50-1675422971675537418,81,15641289,185,120,375,0,5088,6989,12375,ENST00000370509.5cmplcmpl2,0,0,0,mRNAENSG00000143162.9CREG1protein_codingENSP00000359540.4NM_003851.3GeneID:8804NP_003842.1MANE Select

MANE v1.0 (mane) Track Description
 

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