Non-Mouse RefSeq Gene
 

Non-Mouse RefSeq Gene slc25a21.L

RefSeq: NM_001097058.1   Status: Provisional
Description: Xenopus laevis solute carrier family 25 (mitochondrial oxoadipate carrier), member 21 L homeolog (slc25a21.L), mRNA; nuclear gene for mitochondrial product.
Organism: Xenopus laevis
UCSC browser: NM_001097058 on African clawed frog (xenLae2)
Entrez Gene: 779440
PubMed on Gene: slc25a21.L
PubMed on Product: solute carrier family 25 (mitochondrial oxoadipate carrier) member 21 L homeolog

mRNA/Genomic Alignments

BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |   459   73.7%         12     +-  56760598  56975099          NM_001097058   259  1089  1563
Position: chr12:56760598-56975099
Genomic Size: 214502
Strand: -
Gene Symbol: slc25a21.L
CDS Start: complete
CDS End: not complete

Links to sequence:

Data schema/format description and download

Go to Other RefSeq track controls

Data last updated at UCSC: 2020-08-18

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