Discrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population.

ABSTRACT: The protein coding sequences of the human reference genome GRCh38, RefSeq mRNA and UniProt protein databases are sometimes inconsistent with each other, due to polymorphisms in the human population, but the overall landscape of the discordant sequences has not been clarified. In this study, we comprehensively listed the discordant bases and regions between the GRCh38, RefSeq and UniProt reference sequences, based on the genomic coordinates of GRCh38. We observed that the RefSeq sequences are more likely to represent the major alleles than GRCh38 and UniProt, by assigning the alternative allele frequencies of the discordant bases. Since some reference sequences have minor alleles, functional and structural annotations may be performed based on rare alleles in the human population, thereby b

SUBMITTER: Shirota M 

PROVIDER: S-EPMC5009343 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature