Well, one approach is to take the longest one. That's what UCSC uses to
call its "canonical transcripts". And restrict to the consensus CDS (CCDS).


On Mon, Nov 25, 2013 at 1:12 PM, array chip <arrayprofile@yahoo.com> wrote:

> Hi all, have another questions about exon genomic coordinates:
>
> library(biomaRt)
> ensembl = useMart("ensembl")
>
> ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
>
> > getBM(attributes =
> c("external_gene_id","chromosome_name","exon_chrom_start","exon_chrom_end","ensembl_transcript_id","rank"), filters
> = 'hgnc_symbol', values=c("KIT"),mart=ensembl)
>
>    chromosome_name exon_chrom_start exon_chrom_end ensembl_transcript_id
> rank
> 1                4         55524085       55524248       ENST00000412167
>  1
> 2                4         55561678       55561947       ENST00000412167
>  2
> 3                4         55564450       55564731       ENST00000412167
>  3
> 4                4         55565796       55565932       ENST00000412167
>  4
> 5                4         55569890       55570058       ENST00000412167
>  5
> 6                4         55573264       55573453       ENST00000412167
>  6
> 7                4         55575590       55575705       ENST00000412167
>  7
> 8                4         55589750       55589864       ENST00000412167
>  8
> 9                4         55592023       55592204       ENST00000412167
>  9
> 10               4         55593384       55593490       ENST00000412167
> 10
> 11               4         55593582       55593708       ENST00000412167
> 11
> 12               4         55593989       55594093       ENST00000412167
> 12
> 13               4         55594177       55594287       ENST00000412167
> 13
> 14               4         55595501       55595651       ENST00000412167
> 14
> 15               4         55597494       55597585       ENST00000412167
> 15
> 16               4         55598037       55598164       ENST00000412167
> 16
> 17               4         55599236       55599358       ENST00000412167
> 17
> 18               4         55602664       55602775       ENST00000412167
> 18
> 19               4         55602887       55602986       ENST00000412167
> 19
> 20               4         55603341       55603446       ENST00000412167
> 20
> 21               4         55604595       55605177       ENST00000412167
> 21
> 22               4         55524085       55524248       ENST00000288135
>  1
> 23               4         55561678       55561947       ENST00000288135
>  2
> 24               4         55564450       55564731       ENST00000288135
>  3
> 25               4         55565796       55565932       ENST00000288135
>  4
> 26               4         55569890       55570058       ENST00000288135
>  5
> 27               4         55573264       55573453       ENST00000288135
>  6
> 28               4         55575590       55575705       ENST00000288135
>  7
> 29               4         55589750       55589864       ENST00000288135
>  8
> 30               4         55592023       55592216       ENST00000288135
>  9
> 31               4         55593384       55593490       ENST00000288135
> 10
> 32               4         55593582       55593708       ENST00000288135
> 11
> 33               4         55593989       55594093       ENST00000288135
> 12
> 34               4         55594177       55594287       ENST00000288135
> 13
> 35               4         55595501       55595651       ENST00000288135
> 14
> 36               4         55597494       55597585       ENST00000288135
> 15
> 37               4         55598037       55598164       ENST00000288135
> 16
> 38               4         55599236       55599358       ENST00000288135
> 17
> 39               4         55602664       55602775       ENST00000288135
> 18
> 40               4         55602887       55602986       ENST00000288135
> 19
> 41               4         55603341       55603446       ENST00000288135
> 20
> 42               4         55604595       55606881       ENST00000288135
> 21
> 43               4         55524106       55524248       ENST00000514582
>  1
> 44               4         55561678       55562072       ENST00000514582
>  2
> 45               4         55595458       55595651       ENST00000512959
>  1
> 46               4         55597494       55597585       ENST00000512959
>  2
> 47               4         55598037       55598164       ENST00000512959
>  3
> 48               4         55599236       55599567       ENST00000512959
>  4
>
> This will give many versions of genomic coordinates. For example, KIT has
> 3 sets of exons. I think these different versions may refer to different
> splicing variants/isoforms. Is there a "default"/"standard" set of exons
> for each gene? and how do I know which one is such one?
>
> Thanks
>
> John
>
>
>
>
> ________________________________
>
> To: Hans-Rudolf Hotz <hrh@fmi.ch>; "bioconductor@r-project.org" <
> bioconductor@r-project.org>
> Sent: Monday, November 25, 2013 12:41 PM
> Subject: Re: [BioC] exon genomic coordinates
>
>
> Hi,
>
> I am trying to use4 bioMart to retrieve the exon coordinates using the
> example provided below:
>
> library(biomaRt)
> ensembl = useMart("ensembl")
>
> ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
>
> getBM(attributes =
> c("chromosome_name","exon_chrom_start","exon_chrom_end","rank"),
> filters = 'hgnc_symbol', values=c("KIT"),mart=ensembl)
>
> The above works fine. However, when I tried to add "hgnc_symbol" to the
> attributes list, it gave me error:
>
> getBM(attributes =
>
> c("hgnc_symbol","chromosome_name","exon_chrom_start","exon_chrom_end","rank"),
> filters = 'hgnc_symbol', values=c("KIT"),mart=ensembl)
>
>
> Error in getBM(attributes = c("hgnc_symbol", "chromosome_name",
> "exon_chrom_start",  :
>   Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple
> attribute pages are not allowed
>
> But if I keep "hgnc_symbol" in the atributes list and
> remove "exon_chrom_start" and "exon_chrom_end", then it worked again:
> getBM(attributes =
> c("hgnc_symbol","chromosome_name","ensembl_transcript_id","rank"),
> filters = 'hgnc_symbol', values=c("KIT"),mart=ensembl)
>
> Can anyone tell me why is that?
>
> Thanks
>
> John
>
>
> ________________________________
> From: Hans-Rudolf Hotz <hrh@fmi.ch>
>
> onductor@r-project.org>
> Sent: Thursday, November 21, 2013 5:38 AM
> Subject: Re: [BioC] exon genomic coordinates
>
>
> Hi John
>
> You can use the BioMart database, which you can access with the biomaRt
> package to get all exons for all transcripts for a given giene, eg:
>
> library(biomaRt)
> ensembl = useMart("ensembl")
> #assuming you are interested in mouse
> mouse.ensembl = useDataset("mmusculus_gene_ensembl",mart=ensembl)
>
> getBM(attributes =
>
> c("chromosome_name","exon_chrom_start","exon_chrom_end","ensembl_exon_id","ensembl_transcript_id","ensembl_gene_id"),
> filters = 'mgi_symbol', values=c("KIT"),mart=mouse.ensembl)
>
>
> Hope this helps
>
> Hans-Rudolf
>
>
> On 11/21/2013 09:14 AM, array chip wrote:
> > Hi,
> >
> >
> > Can anyone suggest how to retrieve the genomic coordinates for all exons
> for a given gene by say gene symbol? For example, how to retrieve the
> coordinates for all 21 exons for gene KIT?
> >
> > Thanks
> >
> > John
> >     [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
> >
>     [[alternative HTML version deleted]]
>
>
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>
>
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