How I can explain the difference in gene size in hg19 and NG genome coordinates?
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4.3 years ago
r.tor ▴ 50

I was looking at the gene coordinates of LDLR for the hg19 and NG assembly in order to convert them to each other, while I do understand the length of the gene may be different in the two assemblies, I fail to understand why should there be a difference in the length of the same gene in the two assemblies. I do appreciate if someone can clarify it to me.

coding NGS Assembly gene next-gen • 1.1k views
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"NG" ?

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I am going to convert coordinates from RefSeqGene NG to Hg19 genome assembly and vice versa and in the case of NG, I mean is an accession number with NG_ prefix which representing genomic regions to support more comprehensive genome-level annotation.

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I don't know the answer to your question, but according to RefSeq, NG_ represents an incomplete genomic region. See

https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/?report=objectonly

I would guess that since Hg19 is UCSC, and RefSeq is NCBI, they each use their own different annotation methods to decide where the genes start and end.

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Thanks so much for the response anyway. I've already checked the NCBI Handbook.

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