RefSeq mRNAs Track Settings
 
RefSeq mRNAs mapped to this assembly   (All mRNA and EST tracks)

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Label: RefSeq accession id    gene name    species of origin of the mRNA   

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Data schema/format description and download
Assembly: Human Jan. 2022 (T2T CHM13v2.0/hs1)

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