Question: Gene Position c.
gravatar for L_LANKA
6 months ago by
L_LANKA0 wrote:

Hello! I have some problem with SNP. So, I have information about localization this SNP on chromosome: 11:g.103301489C>A. c.-215C>A I understand that this is the 11 Chr and 103301489 nucleotide but I don`t understand what means c.-215C>A. If you have some information or manual about it, I will be so happy if you give me this information!!!

snp • 143 views
ADD COMMENTlink modified 6 months ago by _r_am32k • written 6 months ago by L_LANKA0

See this page for hgvs record format explanation. Specifically this section.

ADD REPLYlink modified 6 months ago • written 6 months ago by GenoMax94k
gravatar for _r_am
6 months ago by
Baylor College of Medicine, Houston, TX
_r_am32k wrote:

The coding reference sequence identifier is missing from the string. Similar to chr11 before the g., there should be a NM_ or ENST identifier before the c. notation that is missing here. Where did you get this string from?

ADD COMMENTlink written 6 months ago by _r_am32k

This information from book about genetics of cows

ADD REPLYlink written 6 months ago by L_LANKA0

It's definitely missing a critical piece of information. It is common practice to omit the reference sequence identifier when the broader context is known - if a particular gene is being discussed, for example. But without context, that notation makes no sense. You might want to search dbSNP/EnsEMBL/other databases by chromosome coordinate to get to that entry though - that might work.

EDIT: I went on Google and looked for a cow genes database and found one at Searching by coordinate there takes me to this entry:

It lies within this feature (is it a gene? I'm not sure, I work on Human genes):

Hope this helps.

ADD REPLYlink modified 6 months ago • written 6 months ago by _r_am32k

Hello L_LANKA,

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work.


ADD REPLYlink written 6 months ago by _r_am32k
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