Schema for MANE - MANE Select Plus Clinical: Representative transcript from RefSeq & GENCODE

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field

example

description

chrom

chr1

Reference sequence chromosome or scaffold

chromStart

166069298

Start position in chromosome

chromEnd

166167001

End position in chromosome

name

ENST00000354422.4

Ensembl id

score

Score (0-1000)

strand

+ or - for strand

thickStart

166070240

Start of where display should be thick (start codon)

thickEnd

166166248

End of where display should be thick (stop codon)

reserved

8,81,156

RGB value (use R,G,B string in input file)

blockCount

Number of blocks

blockSizes

1465,1016,

Comma separated list of block sizes

chromStarts

0,96687,

Start positions relative to chromStart

name2

ENST00000354422.4

Alternative/human readable name

cdsStartStat

cmpl

Status of CDS start annotation (none, unknown, incomplete, or complete)

cdsEndStat

cmpl

Status of CDS end annotation (none, unknown, incomplete, or complete)

exonFrames

2,0,

Exon frame {0,1,2}, or -1 if no frame for exon

type

mRNA

Transcript type

geneName

ENSG00000188859.7

Ensembl Gene identifier

geneName2

FAM78B

Gene symbol

geneType

protein_coding

Gene type

ensemblProtAcc

ENSP00000346404.3

Ensembl protein identifier, none for noncoding

ncbiId

NM_001017961.5

NCBI id

ncbiGene

GeneID:149297

NCBI gene

ncbiProtAcc

NP_001017961.1

NCBI protein identifier, none for noncoding

maneStat

MANE Select

MANE transcript status

chrom

chromStart

chromEnd

name

score

strand

thickStart

thickEnd

reserved

blockCount

blockSizes

chromStarts

name2

cdsStartStat

cdsEndStat

exonFrames

type

geneName

geneName2

geneType

ensemblProtAcc

ncbiId

ncbiGene

ncbiProtAcc

maneStat

chr1

166069298

166167001

ENST00000354422.4

166070240

166166248

8,81,156

1465,1016,

0,96687,

ENST00000354422.4

cmpl

2,0,

mRNA

ENSG00000188859.7

FAM78B

protein_coding

ENSP00000346404.3

NM_001017961.5

GeneID:149297

NP_001017961.1

MANE Select

chr1

166839474

166856359

ENST00000367876.9

166840956

166850409

8,81,156

130,134,127,99,1486,3775,

0,1480,7137,8019,9463,13110,

ENST00000367876.9

cmpl

-1,0,0,1,1,-1,

mRNA

ENSG00000143157.12

POGK

protein_coding

ENSP00000356850.4

NM_017542.5

GeneID:57645

NP_060012.3

MANE Select

chr1

166856509

166876264

ENST00000367874.5

166857566

166876233

8,81,156

1210,163,152,210,98,66,92,105,

0,1609,3676,5693,7314,12935,13253,19650,

ENST00000367874.5

cmpl

0,2,0,0,1,1,2,0,

mRNA

ENSG00000152382.6

TADA1

protein_coding

ENSP00000356848.4

NM_053053.4

GeneID:117143

NP_444281.1

MANE Select

chr1

166908186

166975540

ENST00000271417.8

166919354

166975268

8,81,156

11204,673,217,114,177,147,57,120,333,318,

0,12520,14406,18880,27114,28404,31327,48546,49582,67036,

ENST00000271417.8

cmpl

0,2,1,1,1,1,1,1,1,0,

mRNA

ENSG00000143195.13

ILDR2

protein_coding

ENSP00000271417.2

NM_199351.3

GeneID:387597

NP_955383.1

MANE Select

chr1

166989279

167022214

ENST00000367872.9

166989352

167021855

8,81,156

205,93,100,156,42,125,55,142,63,133,76,547,

0,457,2098,3406,4748,14900,15796,15976,26942,28547,31805,32388,

ENST00000367872.9

cmpl

0,0,0,1,1,1,0,1,2,2,0,1,

mRNA

ENSG00000143194.13

MAEL

protein_coding

ENSP00000356846.4

NM_032858.3

GeneID:84944

NP_116247.1

MANE Select

chr1

167052835

167090377

ENST00000367868.4

167054333

167090287

8,81,156

1631,136,120,156,217,155,133,

0,2140,2894,10746,16086,20549,37409,

ENST00000367868.4

cmpl

2,1,1,1,0,1,0,

mRNA

ENSG00000143167.12

GPA33

protein_coding

ENSP00000356842.3

NM_005814.3

GeneID:10223

NP_005805.1

MANE Select

chr1

167094074

167129165

ENST00000361200.7

167094849

167128608

8,81,156

120,126,95,232,218,3379,

0,759,19635,23253,25174,31712,

ENST00000361200.7

cmpl

-1,0,2,1,2,1,

mRNA

ENSG00000198842.10

STYXL2

protein_coding

ENSP00000354483.2

NM_001080426.3

GeneID:92235

NP_001073895.1

MANE Select

chr1

167220885

167427340

ENST00000367866.7

167220897

167415810

8,81,156

73,66,101,54,120,189,127,95,174,142,140,180,106,346,89,11841,

0,111584,144581,149275,151031,153222,155143,162971,168702,175400,177108,178300,180565,191073,192140,194614,

ENST00000367866.7

cmpl

0,1,1,0,0,0,0,1,0,0,1,0,0,1,2,1,

mRNA

ENSG00000143190.23

POU2F1

protein_coding

ENSP00000356840.2

NM_002697.4

GeneID:5451

NP_002688.3

MANE Select

chr1

167430639

167518529

ENST00000362089.10

167431680

167518465

8,81,156

1107,36,57,36,81,57,104,122,

0,2384,3380,4759,7930,8704,10024,87768,

ENST00000362089.10

cmpl

0,0,0,0,0,0,1,0,

mRNA

ENSG00000198821.12

CD247

protein_coding

ENSP00000354782.5

NM_198053.3

GeneID:919

NP_932170.1

MANE Select

chr1

167541012

167553762

ENST00000370509.5

167542297

167553741

8,81,156

1289,185,120,375,

0,5088,6989,12375,

ENST00000370509.5

cmpl

2,0,0,0,

mRNA

ENSG00000143162.9

CREG1

protein_coding

ENSP00000359540.4

NM_003851.3

GeneID:8804

NP_003842.1

MANE Select

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.

This track is automatically updated, see the source data version above for the current version number. MANE include almost all human protein-coding genes and genes of clinical relevance, including genes in the American College of Medical Genetics and Genomics (ACMG) Secondary Findings list (SF) v3.0. It includes both MANE Select and MANE Plus Clinical 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.bb stdout

Download links for MANE: 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