Get a list of human genes that are known to have introns within the 5'UTR

Question

[nash.claire]

Hi all,

I wondered if anyone knows of a way to take all the genes in the human genome and pull out all of those that feature introns within the 5'UTRs?? Here is an example of the type of gene/transcript that I'm talking about (although this link is for the hg19 genome build)

http://grch37.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000137936;r=1:94027347-94312706;t=ENST00000370244

You can see from the ensembl entry that the 5'UTR (in red) is broken up by 3 introns (faded grey). If possible, I'd like to pull out all the genes in the genome that look like this (ie have 1 or more introns within the 5"UTR)

Any ideas?

Answer 1

[Pierre Lindenbaum]

Using the UCSC/gencode and the following awk script:

BEGIN   {
    FS="\t";
    }

    {
    strand = $4;
    txStart = int($5);
    txEnd = int($6);
    cdsStart = int($7);
    cdsEnd = int($8);
    exonCount = int($9);

    split($10,exonStarts,/[,]/);
    split($11,exonEnds,/[,]/);

    for(i=1;i+1<=exonCount;++i)
        {
        intronStart = int(exonEnds[i]);
        intronEnd = int(exonStarts[i+1]);
        if( (strand == "+" && intronEnd <= cdsStart)  || (strand == "-" && intronStart >= cdsEnd)  )
            {
            print;
            next;
            }
        }
    }

.

$ curl -s  "http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/wgEncodeGencodeCompV24.txt.gz" | gunzip -c |awk -f biostar.awk 

585 ENST00000417324.1   chr1    -   34553   36081   34553   34553   3   34553,35276,35720,  35174,35481,36081,  0   FAM138A none    none    -1,-1,-1,
585 ENST00000461467.1   chr1    -   35244   36073   35244   35244   2   35244,35720,    35481,36073,    0   FAM138A none    none    -1,-1,
585 ENST00000466430.5   chr1    -   89294   120932  89294   89294   4   89294,92090,112699,120774,  91629,92240,112804,120932,  0   RP11-34P13.7    none    none    -1,-1,-1,-1,
585 ENST00000495576.1   chr1    -   89550   91105   89550   89550   2   89550,90286,    90050,91105,    0   RP11-34P13.8    none    none    -1,-1,
585 ENST00000477740.5   chr1    -   92229   129217  92229   92229   4   92229,112699,120720,129054, 92240,112804,120932,129217, 0   RP11-34P13.7    none    none    -1,-1,-1,-1,
585 ENST00000471248.1   chr1    -   110952  129173  110952  110952  3   110952,112699,129054,   111357,112804,129173,   0   RP11-34P13.7    none    none    -1,-1,-1,
73  ENST00000610542.1   chr1    -   120724  133723  120724  120724  4   120724,120873,129054,133373,    120869,120932,129223,133723,    0   RP11-34P13.7    none    none    -1,-1,-1,-1,
73  ENST00000453576.2   chr1    -   129080  133566  129080  129080  2   129080,133373,  129223,133566,  0   RP11-34P13.7    none    none    -1,-1,
586 ENST00000493797.1   chr1    -   139789  140339  139789  139789  2   139789,140074,  139847,140339,  0   RP11-34P13.14   none    none    -1,-1,
586 ENST00000484859.1   chr1    -   141473  149707  141473  141473  2   141473,146385,  143011,149707,  0   RP11-34P13.13   none    none    -1,-1,
586 ENST00000490997.5   chr1    -   142807  146831  142807  142807  3   142807,146385,146641,   143011,146509,146831,   0   RP11-34P13.13   none    none    -1,-1,-1,
586 ENST00000466557.6   chr1    -   146385  173862  146385  146385  8   146385,155766,164262,165883,168099,169048,172556,173752,    146509,155831,164791,165942,168165,169264,172688,173862,    0   RP11-34P13.13   none    none    -1,-1,-1,-1,-1,-1,-1,-1,
586 ENST00000491962.1   chr1    -   165888  168767  165888  165888  3   165888,168099,168609,   165942,168165,168767,   0   RP11-34P13.13   none    none    -1,-1,-1,
73  ENST00000442116.1   chr1    -   257863  264733  257863  257863  2   257863,264603,  259025,264733,  0   AP006222.2  none    none    -1,-1,
73  ENST00000448958.1   chr1    -   258143  268807  258143  258143  3   258143,267302,268666,   259025,268204,268807,   0   AP006222.2  none    none    -1,-1,-1,
73  ENST00000634344.1   chr1    -   258500  267911  258500  258500  3   258500,261549,267302,   259025,261634,267911,   0   AP006222.2  none    none    -1,-1,-1,
587 ENST00000424587.6   chr1    -   266360  297502  266360  266360  4   266360,268666,289265,297344,    268204,268816,289370,297502,    0   AP006222.2  none    none    -1,-1,-1,-1,
587 ENST00000335577.4   chr1    -   287516  289370  287516  287516  2   287516,289265,  287921,289370,  0   AP006222.2  none    none    -1,-1,
587 ENST00000441866.1   chr1    -   357382  359681  357382  357382  3   357382,358048,359344,   357586,358183,359681,   0   RP5-857K21.15   none    none    -1,-1,-1,
587 ENST00000431321.1   chr1    -   365388  366120  365388  365388  2   365388,366018,  365692,366120,  0   RP4-669L17.10   none    none    -1,-1,

Answer 2

[nash.claire]

Wow that's awesome it worked beautifully. Thanks Pierre!

[WouterDeCoster]

Please use ADD COMMENT to reply to earlier answers, as such this thread remains logically structured and easy to follow. In addition, don't forget to upvote when an answer was helpful and accept the answer if your question is resolved.

[nash.claire]

Sorry it's been a long day. Next time I'll do it right.

[Pierre Lindenbaum]

  :-)

[nash.claire]

Hahaha if this leads to a paper in any way I'll be surprised! But noted!!

Answer 3

[nash.claire]

Just to add, if using Pierre's script above, I added an additional step to only pull out the transcripts that have a protein coding biotype. This is easily done using Biomart in R.