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Database: hg38 Primary Table: xenoRefGene Row Count: 200,365 Data last updated: 2020-08-17
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
| field | example | SQL type | info | description |
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| bin | 596 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| name | NM_001123207 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
| chrom | chr6_GL000254v2_alt | varchar(255) | values | Reference sequence chromosome or scaffold |
| strand | + | char(1) | values | + or - for strand |
| txStart | 1515909 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
| txEnd | 1516401 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
| cdsStart | 1515909 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
| cdsEnd | 1516401 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
| exonCount | 3 | int(10) unsigned | range | Number of exons |
| exonStarts | 1515909,1515993,1516233, | longblob | | Exon start positions (or end positions for minus strand item) |
| exonEnds | 1515960,1516191,1516401, | longblob | | Exon end positions (or start positions for minus strand item) |
| score | 0 | int(11) | range | score |
| name2 | TRIM10 | varchar(255) | values | Alternate name (e.g. gene_id from GTF) |
| cdsStartStat | incmpl | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS start annotation (none, unknown, incomplete, or complete) |
| cdsEndStat | incmpl | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS end annotation (none, unknown, incomplete, or complete) |
| exonFrames | 0,0,0, | longblob | | Reading frame of the start of the CDS region of the exon, in the direction of transcription (0,1,2), or -1 if there is no CDS region. |
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To download this table in different text formats or to intersect or correlate it with other tables, use the Table Browser.
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Connected Tables and Joining Fields
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hg38.all_est.qName (via xenoRefGene.name)
hg38.all_mrna.qName (via xenoRefGene.name)
hg38.refGene.name (via xenoRefGene.name)
hg38.refSeqAli.qName (via xenoRefGene.name)
hg38.xenoEst.qName (via xenoRefGene.name)
hg38.xenoMrna.qName (via xenoRefGene.name)
hg38.xenoRefFlat.name (via xenoRefGene.name)
hg38.xenoRefSeqAli.qName (via xenoRefGene.name)
hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
hgFixed.gbSeq.acc (via xenoRefGene.name)
hgFixed.gbWarn.acc (via xenoRefGene.name)
hgFixed.imageClone.acc (via xenoRefGene.name)
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Sample Rows
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| bin | name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | exonCount | exonStarts | exonEnds | score | name2 | cdsStartStat | cdsEndStat | exonFrames |
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| 596 | NM_001123207 | chr6_GL000254v2_alt | + | 1515909 | 1516401 | 1515909 | 1516401 | 3 | 1515909,1515993,1516233, | 1515960,1516191,1516401, | 0 | TRIM10 | incmpl | incmpl | 0,0,0, |
| 83 | NM_001039863 | chr12 | - | 10806236 | 11078188 | 10806236 | 11078188 | 4 | 10806236,10825891,10826086,11078107, | 10806410,10825996,10826137,11078188, | 0 | T2R22 | incmpl | incmpl | 0,0,0,0, |
| 73 | NM_001039863 | chr12_GL877876v1_alt | - | 4942 | 137844 | 4942 | 137844 | 4 | 4942,8373,24792,137778, | 5116,8508,24843,137844, | 0 | T2R22 | incmpl | incmpl | 0,0,0,0, |
| 73 | NM_001039863 | chr12_KI270904v1_alt | - | 532 | 185499 | 532 | 185499 | 5 | 532,5248,24676,24792,185418, | 703,5384,24702,24843,185499, | 0 | T2R22 | incmpl | incmpl | 0,2,0,0,0, |
| 2080 | NM_001077112 | chr2 | - | 196063297 | 196063974 | 196063306 | 196063963 | 3 | 196063297,196063612,196063636, | 196063607,196063630,196063974, | 0 | GSTA3 | cmpl | cmpl | 2,2,0, |
| 1112 | NM_001080366 | chrX | - | 69160861 | 69165454 | 69161305 | 69163073 | 7 | 69160861,69161039,69161310,69161888,69161984,69162517,69165397, | 69161003,69161309,69161888,69161918,69162514,69163141,69165454, | 0 | PJA1 | cmpl | cmpl | -1,2,0,0,1,1,-1, |
| 585 | NM_001000367 | chr1 | + | 52451 | 63827 | 52451 | 63827 | 2 | 52451,63105, | 52608,63827, | 0 | Olr752 | cmpl | incmpl | 0,1, |
| 585 | NM_001000613 | chr1 | + | 52451 | 63853 | 52451 | 63853 | 2 | 52451,63110, | 52613,63853, | 0 | Olr757 | cmpl | incmpl | 0,0, |
| 1682 | NM_072896 | chr1 | - | 143905555 | 143905966 | 143905555 | 143905966 | 1 | 143905555, | 143905966, | 0 | his-17 | cmpl | cmpl | 0, |
| 585 | NM_001000369 | chr1 | + | 62949 | 63887 | 62949 | 63887 | 1 | 62949, | 63887, | 0 | Olr758 | incmpl | cmpl | 1, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Other RefSeq (xenoRefGene) Track Description
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Description
The RefSeq mRNAs gene track for the mouse (Jun. 2020 (GRCm39/mm39))
genome assembly displays translated blat alignments of vertebrate and
invertebrate mRNA in
GenBank.
Track statistics summary
Total genome size: 2,654,624,157 (not counting gaps)
Gene count: 22,442
Bases in genes: 838,462,469 (txStart to txEnd)
Genes percent genome coverage: % 31.585
Bases in exons: 53,564,706
Exons percent genome coverage: % 2.018
Search tips
Please note, the name searching system is not completely case insensitive.
When in doubt, enter search names in all lower case to find gene names.
Methods
The mRNAs were aligned against the mouse (Jun. 2020 (GRCm39/mm39)) genome using
translated blat. When a single mRNA aligned in multiple places, the alignment
having the highest base identity was found. Only those alignments having a base
identity level within 1% of the best and at least 25% base identity with the
genomic sequence were kept.
Specifically, the translated blat command is:
blat -noHead -q=rnax -t=dnax -mask=lower target.fa query.fa target.query.psl
where target.fa is one of the chromosome sequence of the genome assembly,
and the query.fa is the mRNAs from RefSeq
The resulting PSL outputs are filtered:
pslCDnaFilter -minId=0.35 -minCover=0.25 -globalNearBest=0.0100 -minQSize=20 \
-ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap \
all.results.psl mm39.xenoRefGene.psl
The filtered mm39.xenoRefGene.psl is converted to
genePred data to display for this track.
Credits
The mRNA track was produced at UCSC from mRNA sequence data
submitted to the international public sequence databases by
scientists worldwide.
References
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.
GenBank.
Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42.
PMID: 23193287; PMC: PMC3531190
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.
GenBank: update.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.
PMID: 14681350; PMC: PMC308779
Kent WJ.
BLAT - the BLAST-like alignment tool.
Genome Res. 2002 Apr;12(4):656-64.
PMID: 11932250; PMC: PMC187518
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