I'm looking for SNPs in BRCA1 and their affect , is there any manual to describe the comments written under the sequences in NCBI ?
and also is there any way to get BRCA1 promoter or coding sequences as a training data set for Neural networks ?
e.g. :
Chromosome: 17:43092418
Gene:BRCA1 (GeneView)
Functional Consequence: intron variant,missense,nc transcript variant
Allele Origin: G(somatic)/A(germline,somatic)
Clinical significance: Benign
Validated: by 1000G,by cluster,by frequency,by hapmap
Global MAF:C=0.3357/1681
red "C/T/G/A" means that all four nucleotides are met in the SNP position in 4 different alleles for this locus
Dear Alex,
it will be self-explanatory to you, if you have a look at the BRCA1 gene at ensembl.org. Restrict your view to missense mutants ("Configure this page") for which you have searched specifically at NCBI. Now you locate the upper SNP of your result table and click the A in position 3232. It will show you that all variants have been found resulting in amino acids E, V, G, or A.
http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000012048;r=17:43044295-43125483;t=ENST00000357654
at that specific point, there may be one of the four red Nucleotides. may be different in different individuals.
At this position, the nucleotide may be A, G, T or C. It can differt from one individual to another.
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