Do you need to work with variant data mapped to historical human RefSeq transcript versions? To make it easier to map your data to the current GRCh38 reference genome and MANE transcripts, we’re now providing a collection of RefSeq transcript alignments including both the latest versions in the GCF_000001405.40-RS_2023_03 annotation release, and older transcripts going back to 1999. The data are available for download from the FTP site.
As shown in the example below (Image 1), you can view these alignments in the Genome Data Viewer by loading the remote bam track (GCF_00001405-RS_2023_03_knownrefseqs_aln.bam) from the FTP site.
Image 1: A view of the annotated RefSeq alignments to the LRIF1 gene, showing the updates to NM_01832 and NM_018372 over time.
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The NCBI’s Variation Services application programming interfaces (APIs) allow you to map to old RefSeq transcripts or GRCh37/hg19 and search and obtain variant data using different notations and file formats.
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If you have questions or would like to provide feedback, please reach out to us at: firstname.lastname@example.org.