Convert Gene location from one human genome build to another

Question

[akij]

I have some genes list and I need to find the chromosome position of those genes. I found 2 web service for this, ncbi and ensembl. As you can see, I search for the gene location TP53 and both website and they give different locations.

ncbi location:       chr17:7668402-7687550 GRCh38.p7
ensembl location:    Chromosome 17: 7,661,779-7,687,550 GRCh38.p10

Now the locations are different. This is probably because they have different build GRCh38.p7 and GRCh38.p10. But the strange thing is ncbi shows gene length is around 2Mb long but ensembl shows that gene is 25Mb long. I don't understand why. It would be nice if someone could point me which one is showing the correct location.

Anyway, I also need those gene locations in GRCh38.p0 instead of GRCh38.p7 or GRCh38.p10. How can i do this?

Answer 1

[cnvspam]

I think the difference between the two would be the number of transcripts for each gene. Frankish et al. show the differences between the two sets (here GENCODE uses Ensembl transcripts). I think you should pick one set and stick with it. I also think RefSeq 's goal is to generate a consensus for a gene, which may explain the different positions.

Take a look at liftOver if you want to convert between two builds. You may have to generate chain files though.

Answer 2

[Petr Ponomarenko]

Please correct me if I am wrong, but GRCh38.p0, GRCh38.p7 and GRCh38.p10 use the same NC_000017.11 for chr17 so coordinates are the same. The difference between NCBI and ENSEMBL is in which transcripts are considered for a given gene. In the end, your selection will depend on the end goal. For human clinical genetics, RefSeq became the standard for reporting and publishing as it is recommended by HGVS notation and HGVS notation is recommended my ACMG. For research purposes, some transcripts in ENSEMBL are very useful and at the same time are not part of RefSeq (yet?).