Mapping Snps To Intron / Exon Number Using Dbsnp Identifiers
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Entering edit mode
12.4 years ago

Is there any tool that can point me to exact number of exon / intron where my SNP is located (Intron-1, Intron-2 etc. ) ?

Why I want to do this: First and last introns are most likely to effect mRNA levels (See: http://rnajournal.cshlp.org/content/9/5/607.full for a background) I want to check whether my SNPs are encoded in first or last introns.

List of sample SNPs: 

rs1354034
rs1344142
rs10866003
rs11130549
rs2133886
rs3184504

I have several thousands of SNPs, so a programmable solution will be ideal.

dbsnp snp intron exon mapping • 5.5k views
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1
Entering edit mode
12.4 years ago

Here I will use 3 tools from my "variation toolkit" :

  • mysqlquery: query a mysql database using the column of a table. Here I will query the position of your snp in UCSC/snp132
  • mysqlucsc: finds the genomic features from table in the UCSC. (knownGene)
  • verticalize: verticalize the result

and a simple awk script.

The script:

VARKIT=/path/to/variationtoolkit/bin
SQLCFG="--host genome-mysql.cse.ucsc.edu --user genome --database hg19"
${VARKIT}/mysqlquery ${SQLCFG} -e 'select chrom,chromStart from snp132 where name="$1"' |\
${VARKIT}/mysqlucsc -1 ${SQLCFG} -T knownGene -C 2 -S 3 -E 3 |\
awk -F '    ' '
/^#/    {printf("%s\tEXON\tcount(EXONS)\n",$0);next;}
    {
    printf("%s\t",$0);
    posSnp=int($3);
    nExons=int($11);
    split($12,exonStarts,"[,]");
    split($13,exonEnds,"[,]");

    for(i=1;i<=nExons;i++)
        {
        if(posSnp>=int(exonStarts[i]) && posSnp< int(exonEnds[i]))
            {
            if($6=="+")
                {
                printf("Exon %d\t%d\n",i,nExons);
                }
            else
                {
                printf("Exon %d\t%d\n",(nExons+1)-i,nExons);
                }
            next;
            }
        }
    printf(".\t.\n");   
    }' |\
${VARKIT}/verticalize

Usage:

cat snp.txt | sh biostar15405.sh

Result (the two last column gives you the Exon n° and the number of exons)

>>> 2
$1  #SNP_ID         rs1354034
$2  chrom           chr3
$3  chromStart      56849748
$4  name            uc011bew.1
$5  chrom           chr3
$6  strand          -
$7  txStart         56761445
$8  txEnd           56950499
$9  cdsStart        56763297
$10 cdsEnd          56950369
$11 exonCount       11
$12 exonStarts      56761445,56766265,56771212,56779232,56785083,56785327,56787531,56789008,56807736,56916319,56950336,
$13 exonEnds        56763650,56766452,56771383,56779490,56785160,56785424,56787594,56789179,56807844,56916382,56950499,
$14 proteinID       Q9NR81-2
$15 alignID         uc011bew.1
$16 EXON            .
$17 count(EXONS)    .
<<< 2

>>> 3
$1  #SNP_ID         rs1354034
$2  chrom           chr3
$3  chromStart      56849748
$4  name            uc003dih.2
$5  chrom           chr3
$6  strand          -
$7  txStart         56761445
$8  txEnd           57113336
$9  cdsStart        56763297
$10 cdsEnd          57069177
$11 exonCount       13
$12 exonStarts      56761445,56766265,56771212,56779232,56785083,56785327,56787531,56789008,56807736,56916319,56992850,57069115,57113253,
$13 exonEnds        56763650,56766452,56771383,56779490,56785160,56785424,56787594,56789179,56807844,56916382,56992917,57069204,57113336,
$14 proteinID       Q9NR81-2
$15 alignID         uc003dih.2
$16 EXON            .
$17 count(EXONS)    .
<<< 3

>>> 4
$1  #SNP_ID         rs1344142
$2  chrom           chr3
$3  chromStart      56857432
$4  name            uc011bew.1
$5  chrom           chr3
$6  strand          -
$7  txStart         56761445
$8  txEnd           56950499
$9  cdsStart        56763297
$10 cdsEnd          56950369
$11 exonCount       11
$12 exonStarts      56761445,56766265,56771212,56779232,56785083,56785327,56787531,56789008,56807736,56916319,56950336,
$13 exonEnds        56763650,56766452,56771383,56779490,56785160,56785424,56787594,56789179,56807844,56916382,56950499,
$14 proteinID       Q9NR81-2
$15 alignID         uc011bew.1
$16 EXON            .
$17 count(EXONS)    .
<<< 4

>>> 5
$1  #SNP_ID         rs1344142
$2  chrom           chr3
$3  chromStart      56857432
$4  name            uc003dih.2
$5  chrom           chr3
$6  strand          -
$7  txStart         56761445
$8  txEnd           57113336
$9  cdsStart        56763297
$10 cdsEnd          57069177
$11 exonCount       13
$12 exonStarts      56761445,56766265,56771212,56779232,56785083,56785327,56787531,56789008,56807736,56916319,56992850,57069115,57113253,
$13 exonEnds        56763650,56766452,56771383,56779490,56785160,56785424,56787594,56789179,56807844,56916382,56992917,57069204,57113336,
$14 proteinID       Q9NR81-2
$15 alignID         uc003dih.2
$16 EXON            .
$17 count(EXONS)    .
<<< 5

>>> 6
$1  #SNP_ID         rs10866003
$2  chrom           chr3
$3  chromStart      56859423
$4  name            uc011bew.1
$5  chrom           chr3
$6  strand          -
$7  txStart         56761445
$8  txEnd           56950499
$9  cdsStart        56763297
$10 cdsEnd          56950369
$11 exonCount       11
$12 exonStarts      56761445,56766265,56771212,56779232,56785083,56785327,56787531,56789008,56807736,56916319,56950336,
$13 exonEnds        56763650,56766452,56771383,56779490,56785160,56785424,56787594,56789179,56807844,56916382,56950499,
$14 proteinID       Q9NR81-2
$15 alignID         uc011bew.1
$16 EXON            .
$17 count(EXONS)    .
<<< 6

>>> 7
$1  #SNP_ID         rs10866003
$2  chrom           chr3
$3  chromStart      56859423
$4  name            uc003dih.2
$5  chrom           chr3
$6  strand          -
$7  txStart         56761445
$8  txEnd           57113336
$9  cdsStart        56763297
$10 cdsEnd          57069177
$11 exonCount       13
$12 exonStarts      56761445,56766265,56771212,56779232,56785083,56785327,56787531,56789008,56807736,56916319,56992850,57069115,57113253,
$13 exonEnds        56763650,56766452,56771383,56779490,56785160,56785424,56787594,56789179,56807844,56916382,56992917,57069204,57113336,
$14 proteinID       Q9NR81-2
$15 alignID         uc003dih.2
$16 EXON            .
$17 count(EXONS)    .
<<< 7

>>> 8
$1  #SNP_ID         rs11130549
$2  chrom           chr3
$3  chromStart      56880443
$4  name            uc011bew.1
$5  chrom           chr3
$6  strand          -
$7  txStart         56761445
$8  txEnd           56950499
$9  cdsStart        56763297
$10 cdsEnd          56950369
$11 exonCount       11
$12 exonStarts      56761445,56766265,56771212,56779232,56785083,56785327,56787531,56789008,56807736,56916319,56950336,
$13 exonEnds        56763650,56766452,56771383,56779490,56785160,56785424,56787594,56789179,56807844,56916382,56950499,
$14 proteinID       Q9NR81-2
$15 alignID         uc011bew.1
$16 EXON            .
$17 count(EXONS)    .
<<< 8

>>> 9
$1  #SNP_ID         rs11130549
$2  chrom           chr3
$3  chromStart      56880443
$4  name            uc003dih.2
$5  chrom           chr3
$6  strand          -
$7  txStart         56761445
$8  txEnd           57113336
$9  cdsStart        56763297
$10 cdsEnd          57069177
$11 exonCount       13
$12 exonStarts      56761445,56766265,56771212,56779232,56785083,56785327,56787531,56789008,56807736,56916319,56992850,57069115,57113253,
$13 exonEnds        56763650,56766452,56771383,56779490,56785160,56785424,56787594,56789179,56807844,56916382,56992917,57069204,57113336,
$14 proteinID       Q9NR81-2
$15 alignID         uc003dih.2
$16 EXON            .
$17 count(EXONS)    .
<<< 9

>>> 10
$1  #SNP_ID         rs2133886
$2  chrom           chr3
$3  chromStart      56942069
$4  name            uc011bew.1
$5  chrom           chr3
$6  strand          -
$7  txStart         56761445
$8  txEnd           56950499
$9  cdsStart        56763297
$10 cdsEnd          56950369
$11 exonCount       11
$12 exonStarts      56761445,56766265,56771212,56779232,56785083,56785327,56787531,56789008,56807736,56916319,56950336,
$13 exonEnds        56763650,56766452,56771383,56779490,56785160,56785424,56787594,56789179,56807844,56916382,56950499,
$14 proteinID       Q9NR81-2
$15 alignID         uc011bew.1
$16 EXON            .
$17 count(EXONS)    .
<<< 10

>>> 11
$1  #SNP_ID         rs2133886
$2  chrom           chr3
$3  chromStart      56942069
$4  name            uc003dih.2
$5  chrom           chr3
$6  strand          -
$7  txStart         56761445
$8  txEnd           57113336
$9  cdsStart        56763297
$10 cdsEnd          57069177
$11 exonCount       13
$12 exonStarts      56761445,56766265,56771212,56779232,56785083,56785327,56787531,56789008,56807736,56916319,56992850,57069115,57113253,
$13 exonEnds        56763650,56766452,56771383,56779490,56785160,56785424,56787594,56789179,56807844,56916382,56992917,57069204,57113336,
$14 proteinID       Q9NR81-2
$15 alignID         uc003dih.2
$16 EXON            .
$17 count(EXONS)    .
<<< 11

>>> 12
$1  #SNP_ID         rs3184504
$2  chrom           chr12
$3  chromStart      111884607
$4  name            uc001tse.2
$5  chrom           chr12
$6  strand          +
$7  txStart         111843751
$8  txEnd           111889426
$9  cdsStart        111855949
$10 cdsEnd          111886106
$11 exonCount       8
$12 exonStarts      111843751,111855922,111884556,111884745,111884928,111885133,111885459,111885786,
$13 exonEnds        111844081,111856681,111884658,111884837,111885023,111885348,111885631,111889426,
$14 proteinID       B9EGG5
$15 alignID         uc001tse.2
$16 EXON            Exon 3
$17 count(EXONS)    8
<<< 12

>>> 13
$1  #SNP_ID         rs3184504
$2  chrom           chr12
$3  chromStart      111884607
$4  name            uc010syf.1
$5  chrom           chr12
$6  strand          +
$7  txStart         111855912
$8  txEnd           111889426
$9  cdsStart        111855949
$10 cdsEnd          111886106
$11 exonCount       7
$12 exonStarts      111855912,111884556,111884745,111884928,111885133,111885459,111885786,
$13 exonEnds        111856681,111884658,111884837,111885023,111885348,111885631,111889426,
$14 proteinID       B9EGG5
$15 alignID         uc010syf.1
$16 EXON            Exon 2
$17 count(EXONS)    7
<<< 13

>>> 14
$1  #SNP_ID         rs3184504
$2  chrom           chr12
$3  chromStart      111884607
$4  name            uc001tsf.2
$5  chrom           chr12
$6  strand          +
$7  txStart         111855922
$8  txEnd           111889426
$9  cdsStart        111855949
$10 cdsEnd          111886106
$11 exonCount       7
$12 exonStarts      111855922,111884556,111884745,111884925,111885133,111885459,111885786,
$13 exonEnds        111856681,111884658,111884837,111885023,111885348,111885631,111889426,
$14 proteinID       B9EGG5
$15 alignID         uc001tsf.2
$16 EXON            Exon 2
$17 count(EXONS)    7
<<< 14

>>> 15
$1  #SNP_ID         rs3184504
$2  chrom           chr12
$3  chromStart      111884607
$4  name            uc010syg.1
$5  chrom           chr12
$6  strand          +
$7  txStart         111872665
$8  txEnd           111889426
$9  cdsStart        111872705
$10 cdsEnd          111886106
$11 exonCount       7
$12 exonStarts      111872665,111884556,111884745,111884928,111885133,111885459,111885786,
$13 exonEnds        111872831,111884658,111884837,111885023,111885348,111885631,111889426,
$14 proteinID       B7Z7K6
$15 alignID         uc010syg.1
$16 EXON            Exon 2
$17 count(EXONS)    7
<<< 15
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Thanks a lot Pierre.

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Installed "variation toolkit" and tried this, am getting "unknown option '--database'. Tried options including standard -D, but not able to solve the issues. Any pointers to solve this issue ?

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Installed "variation toolkit" and tried this, but am getting "unknown option '--database'. Tried options including standard -D and other variations, but not able to solve this. Any idea how can I solve this ?

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what does 'svn info' says ? the rev number should be >=239

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Thanks, updated to latest version and it is working. I am able to find the number of exon where a given SNPs is present and total number of exons. This is perfect for SNPs in exons, how about SNPs in introns ? May be am missing something ?

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change the awk script: see http://biostar.stackexchange.com/questions/15819

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