Schema for MANE select v0.9 - NCBI RefSeq and Ensembl transcripts from the MANE Project (v0.9)
  Database: hg38    Primary Table: mane Data last updated: 2020-06-01
Big Bed File: /gbdb/hg38/mane/mane.0.9.bb
Item Count: 15,569
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)
reserved222,45,38RGB value (use R,G,B string in input file)
blockCount2Number of blocks
blockSizes1465,1016Comma separated list of block sizes
chromStarts0,96687Start 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)
exonFrames2,0Exon frame {0,1,2}, or -1 if no frame for exon
typeprotein_codingTranscript 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

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsname2cdsStartStatcdsEndStatexonFramestypegeneNamegeneName2geneTypeensemblProtAccncbiIdncbiGenencbiProtAcc
chr1166069298166167001ENST00000354422.40-166070240166166248222,45,3821465,10160,96687ENST00000354422.4cmplcmpl2,0protein_codingENSG00000188859.7FAM78Bprotein_codingENSP00000346404.3NM_001017961.5GeneID:149297NP_001017961.1
chr1166839474166856359ENST00000367876.90+166840956166850409222,45,386130,134,127,99,1486,37750,1480,7137,8019,9463,13110ENST00000367876.9cmplcmpl-1,0,0,1,1,-1protein_codingENSG00000143157.12POGKprotein_codingENSP00000356850.4NM_017542.5GeneID:57645NP_060012.3
chr1166856509166876264ENST00000367874.50-166857566166876233222,45,3881210,163,152,210,98,66,92,1050,1609,3676,5693,7314,12935,13253,19650ENST00000367874.5cmplcmpl0,2,0,0,1,1,2,0protein_codingENSG00000152382.6TADA1protein_codingENSP00000356848.4NM_053053.4GeneID:117143NP_444281.1
chr1166908186166975540ENST00000271417.80-166919354166975268222,45,381011204,673,217,114,177,147,57,120,333,3180,12520,14406,18880,27114,28404,31327,48546,49582,67036ENST00000271417.8cmplcmpl0,2,1,1,1,1,1,1,1,0protein_codingENSG00000143195.13ILDR2protein_codingENSP00000271417.2NM_199351.3GeneID:387597NP_955383.1
chr1166989279167022214ENST00000367872.90+166989352167021855222,45,3812205,93,100,156,42,125,55,142,63,133,76,5470,457,2098,3406,4748,14900,15796,15976,26942,28547,31805,32388ENST00000367872.9cmplcmpl0,0,0,1,1,1,0,1,2,2,0,1protein_codingENSG00000143194.13MAELprotein_codingENSP00000356846.4NM_032858.3GeneID:84944NP_116247.1
chr1167052835167090377ENST00000367868.40-167054333167090287222,45,3871631,136,120,156,217,155,1330,2140,2894,10746,16086,20549,37409ENST00000367868.4cmplcmpl2,1,1,1,0,1,0protein_codingENSG00000143167.12GPA33protein_codingENSP00000356842.3NM_005814.3GeneID:10223NP_005805.1
chr1167094074167129165ENST00000361200.70+167094849167128608222,45,386120,126,95,232,218,33790,759,19635,23253,25174,31712ENST00000361200.7cmplcmpl-1,0,2,1,2,1protein_codingENSG00000198842.10DUSP27protein_codingENSP00000354483.2NM_001080426.3GeneID:92235NP_001073895.1
chr1167220885167427340ENST00000367866.70+167220897167415810222,45,381673,66,101,54,120,189,127,95,174,142,140,180,106,346,89,118410,111584,144581,149275,151031,153222,155143,162971,168702,175400,177108,178300,180565,191073,192140,194614ENST00000367866.7cmplcmpl0,1,1,0,0,0,0,1,0,0,1,0,0,1,2,1protein_codingENSG00000143190.23POU2F1protein_codingENSP00000356840.2NM_002697.4GeneID:5451NP_002688.3
chr1167430639167518529ENST00000362089.100-167431680167518465222,45,3881107,36,57,36,81,57,104,1220,2384,3380,4759,7930,8704,10024,87768ENST00000362089.10cmplcmpl0,0,0,0,0,0,1,0protein_codingENSG00000198821.11CD247protein_codingENSP00000354782.5NM_198053.3GeneID:919NP_932170.1
chr1167541012167553762ENST00000370509.50-167542297167553741222,45,3841289,185,120,3750,5088,6989,12375ENST00000370509.5cmplcmpl2,0,0,0protein_codingENSG00000143162.9CREG1protein_codingENSP00000359540.4NM_003851.3GeneID:8804NP_003842.1

MANE select v0.9 (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.

Note that MANE v0.9 is a beta release and only covers 81% of protein coding genes. RefSeq and Ensembl will continue to develop this single transcript gene set and provide comprehensive sets of alternate transcripts in the RefSeq-All and the GENCODE tracks.

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.0.9.bb stdout

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

Download links for MANE Select v0.9: ftp://ftp.ncbi.nlm.nih.gov/refseq/MANE