Schema for RefSeq mRNAs - RefSeq mRNAs mapped to this assembly
  Database: mm39    Primary Table: xenoMRnas Data last updated: 2020-07-30
Big Bed File: /gbdb/mm39/xenoRefGene/mm39.xenoRefGene.bb
Item Count: 22,442
Format description: bigGenePred gene models
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart129201040Start position in chromosome
chromEnd130147015End position in chromosome
nameNM_172485RefSeq accession id
score0Score (0-1000)
strand++ or - for strand
thickStart129358567Start of where display should be thick (start codon)
thickEnd130145917End of where display should be thick (stop codon)
reserved0RGB value (use R,G,B string in input file)
blockCount29Number of blocks
blockSizes120,140,173,811,249,170,156,198,192,235,116,130,104,195,267,179,134,151,142,116,118,146,160,174,96,81,195,88,1180,Comma separated list of block sizes
chromStarts0,157,157493,322066,339806,355573,394510,404745,485142,486965,502989,543339,549288,642249,647944,678086,829767,843256,886270,889516,891745,907048,915156,916552,916827,919250,921801,936937,944795,Start positions relative to chromStart
name2Alternative/human readable name
cdsStartStatnoneStatus of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStatnoneStatus of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames-1,-1,0,1,2,2,1,1,1,1,2,1,2,1,1,1,0,2,0,1,0,1,0,1,1,1,1,1,2,Exon frame {0,1,2}, or -1 if no frame for exon
typeTranscript type
geneNameThsd7bgene name
geneName2Mus musculusspecies of origin of the mRNA
geneTypeGene type

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsname2cdsStartStatcdsEndStatexonFramestypegeneNamegeneName2geneType
chr1129201040130147015NM_1724850+129358567130145917029120,140,173,811,249,170,156,198,192,235,116,130,104,195,267,179,134,151,142,116,118,146,160,174,96,81,195,88,1180,0,157,157493,322066,339806,355573,394510,404745,485142,486965,502989,543339,549288,642249,647944,678086,829767,843256,886270,889 ...nonenone-1,-1,0,1,2,2,1,1,1,1,2,1,2,1,1,1,0,2,0,1,0,1,0,1,1,1,1,1,2,Thsd7bMus musculus
chr1130316396130350780NM_0078270-13031639613035069501170,21,63,147,192,86,100,192,186,16,127,0,21212,21969,22733,25389,28179,29448,30941,33455,34205,34257,nonenone1,1,1,1,1,2,1,1,1,0,0,Cd55bMus musculus
chr1130366787130390481NM_0100160-130368048130390406013399,46,693,21,81,147,192,86,100,192,186,16,122,0,430,636,8568,9277,10366,13333,17770,19036,20531,22771,23519,23572,nonenone-1,-1,0,0,0,0,0,1,0,0,0,2,0,Cd55Mus musculus
chr1130504442130557343NM_0095810-130504655130547174013102,287,203,90,201,198,183,195,86,100,183,104,71,0,133,1180,6143,6694,14658,19953,22101,22454,38453,41589,42638,52830,nonenone-1,0,1,1,1,1,1,1,2,1,1,0,-1,Zp3rMus musculus
chr1130563657130589355NM_0075760-130563942130585034010450,176,165,180,192,86,97,183,183,171,0,780,3148,7013,12108,12463,17404,19960,21211,25527,nonenone0,1,1,1,1,2,1,1,0,-1,C4bpMus musculus
chr1130597943130611808NM_0169950-1305979951306118080627,142,127,90,176,172,0,52,740,11942,12595,13693,nonenone-1,1,0,0,1,0,C4bpbRattus norvegicus
chr1130616793130644668NM_0010339650-13061881913064229302219,508,135,70,344,835,69,180,65,63,130,105,147,208,125,57,75,67,97,126,111,131,0,47,567,721,842,1257,7960,8849,9622,10131,10924,11713,12648,13174,16320,17369,17786,17995,18452,19019,25409,27744,nonenone-1,-1,-1,-1,-1,0,0,0,1,1,0,0,0,2,0,0,0,2,1,1,0,-1,Pfkfb2Rattus norvegicus
chr1130645063130649792NM_1786910+13064522013064715604485,2304,351,493,0,1389,3829,4236,nonenone0,1,-1,-1,Yod1Mus musculus
chr1130659712130672359NM_1776040+13066531913067160004248,186,181,2294,0,5526,9027,10353,nonenone-1,0,0,1,AA986860Mus musculus
chr1130728638130742477NM_0011706320+1307286861307423900787,226,141,339,757,119,242,0,2149,3641,10469,11689,13092,13597,nonenone0,0,1,1,1,2,1,FcamrMus musculus

RefSeq mRNAs (xenoMRnas) Track Description
 

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