Conflicting sequences between Genome Browser and NCBI (reference hg19).

Question

[dodausp]

Likely some of you has come across such a thing when browsing around DNA or AA sequence, but unfortunately I could not find any resource that explains it.

Problem

I am cross-checking AA sequences between Genome Browser and NCBI platforms, using reference hg19/GRCh37, and have found quite a few discordant sequences between the two. More precisely, different AA's for the same position.

Example

Here are some examples:

Transcript ID   Position    AA (Genome Browser) AA (NCBI)
NM_000937   chr17:7417086           A               T
NM_001145468    chr22:24717850          D                   G
NM_001190441    chr19:40149297          L                   H
NM_001291324    chr17:79409366          G                   R
NM_005126   chr3:24006477           L               M

Also a question associated to that: I understand that when transcripts change their version (e.g. NM_001013356.2 to NM_001013356.3), some single nucleotides also change their sequence. What would be the explanation for that? Would that be because their allele frequency is more representative of a population (based on the ever growing studies with DNA sequence)?

[GenoMax]

Genome Browser at NCBI or some other program?

As for this

I understand that when transcripts change their version (e.g. NM_001013356.2 to NM_001013356.3), some single nucleotides also change their sequence. What would be the explanation for that?

https://www.ncbi.nlm.nih.gov/books/NBK50679/#RefSeqFAQ.what_causes_the_version_number

[dodausp]

Thank you for the link. I did observe that in some of the variants I was looking up - it was good to have the official explanation. Now, those such the ones from the example above, I cannot quite figure out why they are different. Genome Browser as the web-based platform (https://genome-euro.ucsc.edu/) and NCBI as their Nucleotide section (https://www.ncbi.nlm.nih.gov/nuccore).

Answer 1

[Prash]

Assuming it is a NCBI genome browser, pl jot down to versions hg38/hg37 and Refseq are Nona fide sequences.

Second, the _00 ids correspond to hypothetical (XM or NM for a few) and are not annotated well and might be off wrong translational reading frames.

Hope this helps Prash