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, 13:59, 13 December 2009
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| 1. A detailed instruction on using the table browser could be found at [http://genome.ucsc.edu/cgi-bin/hgTables?command=start#Help genome.ucsc.edu/cgi-bin/hgTables]. | | 1. A detailed instruction on using the table browser could be found at [http://genome.ucsc.edu/cgi-bin/hgTables?command=start#Help genome.ucsc.edu/cgi-bin/hgTables]. |
− | 2. One can specify the regieon to be the whole genome or any particular gene position (e.g. chr21:33031597-33041570). | + | 2. One can specify the region to be the whole genome or any particular gene position (e.g. chr21:33031597-33041570). |
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| Here is an example of input gene file headlines: | | Here is an example of input gene file headlines: |
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| 5'UTR=A26C2[-] means the SNP is in the 5'UTR region of gene A26C2 with a minus strand. | | 5'UTR=A26C2[-] means the SNP is in the 5'UTR region of gene A26C2 with a minus strand. |
| INTRONIC=POTEG[-] means the SNP is in the intronic region of gene POTEG with a minus strand. | | INTRONIC=POTEG[-] means the SNP is in the intronic region of gene POTEG with a minus strand. |
− | SYNONYMOUS_CODING=GAB4:Ala15826157Ala[-] means that the SNP is synonymous coding at position 15826157 in gene GAB4 with a minus strand and it keeps amino-acid Ala unchaged. | + | SYNONYMOUS_CODING=GAB4:Ala15826157Ala[-] means that the SNP is synonymous coding at position 15826157 in gene GAB4 with a minus strand and it keeps amino-acid Ala unchanged. |
| NON_SYNONYMOUS_CODING=GAB4:Leu15830952Pro[-] means that the SNP is non_synonymous coding at position 15830925 in gene GAB4 with a minus strand and it changes amino-acid Leu to Pro. | | NON_SYNONYMOUS_CODING=GAB4:Leu15830952Pro[-] means that the SNP is non_synonymous coding at position 15830925 in gene GAB4 with a minus strand and it changes amino-acid Leu to Pro. |
− | SPLICE_SITE=NCAPH2[+] means that the SNP is in the SPLICE_SITE (5 bp within exon start or end positions in the coding reegion) of gene MCAPH2 with a plus strand. | + | SPLICE_SITE=NCAPH2[+] means that the SNP is in the SPLICE_SITE (5 bp within exon start or end positions in the coding region) of gene MCAPH2 with a plus strand. |
| STOP_GAINED=MAPK12:Trp49035685stop[-] means that the SNP is at position 49035685 in gene MAPK12 with a minus strand and it changes amino-acid Trp to a stop codon. | | STOP_GAINED=MAPK12:Trp49035685stop[-] means that the SNP is at position 49035685 in gene MAPK12 with a minus strand and it changes amino-acid Trp to a stop codon. |
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