Schema for RefSeq mRNAs - RefSeq mRNAs mapped to this assembly
  Database: hub_567047_hs1    Primary Table: hub_567047_xenoRefGene Data last updated: 2022-02-07
Big Bed File Download: /gbdb/hs1/bbi/xenoRefGene.bb
Item Count: 20,844
The data is stored in the binary BigBed format.

Format description: bigGenePred gene models
fieldexampledescription
chromCP068254.1Reference sequence chromosome or scaffold
chromStart9112Start position in chromosome
chromEnd9400End position in chromosome
nameNM_126741RefSeq accession id
score0Score (0-1000)
strand++ or - for strand
thickStart9112Start of where display should be thick (start codon)
thickEnd9400End of where display should be thick (stop codon)
reserved0RGB value (use R,G,B string in input file)
blockCount1Number of blocks
blockSizes288,Comma separated list of block sizes
chromStarts0,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)
exonFrames0,Exon frame {0,1,2}, or -1 if no frame for exon
typeTranscript type
geneNameT17H1.13; T17H1_13gene name
geneName2Arabidopsis thalianaspecies of origin of the mRNA
geneTypeGene type

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsname2cdsStartStatcdsEndStatexonFramestypegeneNamegeneName2geneType
CP068254.191129400NM_1267410+9112940001288,0,nonenone0,T17H1.13; T17H1_13Arabidopsis thaliana

RefSeq mRNAs (hub_567047_xenoRefGene) Track Description
 

Description

The RefSeq mRNAs gene track for the 24 Jan 2022 Homo sapiens/GCA_009914755.4_T2T-CHM13v2.0 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.

Track statistics summary

Total genome size: 3,117,292,070
Gene count: 20,844
Bases in genes: 1,125,310,304
Percent genome coverage: % 36.099

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 Homo sapiens/GCA_009914755.4_T2T-CHM13v2.0 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 GCA_009914755.4_T2T-CHM13v2.0.xenoRefGene.psl
The filtered GCA_009914755.4_T2T-CHM13v2.0.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