Question: gene coordinates from TxDb.Hsapiens.UCSC.hg19.knownGene do not match NCBI gene bank
gravatar for yliueagle
6 months ago by
yliueagle220 wrote:

I retrieved gene cordinates from TxDb.Hsapiens.UCSC.hg19.knownGene using:

gene_info = genes(TxDb.Hsapiens.UCSC.hg19.knownGene)

But I found some of the genes, for example, PTPN20 (id: 26095) is hugely different from NCBI gene bank. It is error information or I am doing something wrong?

subset(gene_info, gene_id=='26095')

GRanges object with 1 range and 1 metadata column:
        seqnames            ranges strand |     gene_id
           <Rle>         <IRanges>  <Rle> | <character>
  26095    chr10 46550123-48827924      - |       26095

The gene coordinates I got from gene bank:

gene • 189 views
ADD COMMENTlink modified 6 months ago by genomax80k • written 6 months ago by yliueagle220

It looks like this gene was annotated in two places in hg19 build (;g=ENSG00000204179;r=10:46911396-47002488 look in other assemblies). This seems to have been resolved in hg38, where only one copy is annotated.!/hgnc_id/HGNC:23423

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax80k

Adding on this, see hg19:

enter image description here

ADD REPLYlink written 6 months ago by ATpoint32k
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