Mutation list based on HbVar db and genome build 18
Tue, 02/13/2007 - 08:45 — kmcallenberg
The following file is a tab-delimited list of beta Thalasssemia-related mutations with DNA-based positions relative to the transcription site according to genome build 18. There are 217 mutations listed.
Not all positions are given relative to the transcription start site, especially those describing mutations within codons. An example is a mutation seen in codon 26, at the first nucleotide position (GAG, the G is mutated). The mutation here is denoted as 79G>T. 79 does not refer to the position of the nucleotide from the transcription start site instead it denotes the nucleotide position from the translation start site (ATG) i.e. the mutation occurs at the 79th nucleotide from start of translation. The A of ATG is considered as the 1st nucleotide.
Thank you Shalu -- good eyes. Using existing data like this from HbVar might be quicker in some ways, but as you are pointing out, it would require that we evaluate every mutation in any case. So this is good justification for us to be collecting our data manually and directly from journal articles, as Dr. Khuri is requesting.
Comments
A note of caution
Not all positions are given relative to the transcription start site, especially those describing mutations within codons. An example is a mutation seen in codon 26, at the first nucleotide position (GAG, the G is mutated). The mutation here is denoted as 79G>T. 79 does not refer to the position of the nucleotide from the transcription start site instead it denotes the nucleotide position from the translation start site (ATG) i.e. the mutation occurs at the 79th nucleotide from start of translation. The A of ATG is considered as the 1st nucleotide.
-Shalu
Thank you, noted
Thank you Shalu -- good eyes. Using existing data like this from HbVar might be quicker in some ways, but as you are pointing out, it would require that we evaluate every mutation in any case. So this is good justification for us to be collecting our data manually and directly from journal articles, as Dr. Khuri is requesting.
--Keith