Does anybody know why the same genomic positions can have different (complementary) alleles although they origin from the same reference genome? One example of such behaviour is here:
http://www.ncbi.nlm.nih.gov/clinvar/variation/104/
While NM_ and NG_ reports reference allele "C", NC_ reports "G". However, it is not a rule as some other records have the same reference allele for NM_ and NC_ ...
Thank you for your response,
Jaroslav
NC records are usually provided with respect to the plus (+) strand on the chromosome. NM records can be either strand depending on direction of transcription. NM records are with respect to the coding strand.
Hello!
For example, for rs721917 SNP information (SFTPD gene) in dbSNP (ncbi), we can found:
http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs721917
NC_000010.10:g.81706324A>G
- nucleotide position in reference sequence accessions (RefSeq) for chromosome records by Genome Reference Consortium (GRC) assembly for the human genome (GRCh37) - GenBank -
NC_000010.11:g.79946568A>G
- nucleotide position in reference sequence accessions (RefSeq) for chromosome records by Genome Reference Consortium (GRC) assembly for the human genome (GRCh38) - GenBank -
NM_003019.4:c.92T>C
- nucleotide position in reference sequence accessions (RefSeq) for mRNA records (a transcript corresponds to a processed sequence and, effectively, it depends of the transciption sense)
I hope it was useful!!
Dear Estefania and Gerard,
it helps, thanks a lot. I understand that it depends on the stand (+/-) but I am still not able to find this information in NCBI record. It seems to be in the special column "comp" in "PRIMARY" item but what can I do in case that there is not such an item (if the record has not more sources and "PRIMARY" is not necessary)?
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