[ensembl-dev] how to calculate transcript length ?

[Jay Humphrey]

Length is end - start + 1.
1 2 3 [4 5 6 7 8] 9
start = 4, end = 8
8 - 4 = 4, actually there are 5 residues.

On 31/07/2012 10:39, ?? wrote:
> Hi All
> I wondering how to calculate transcript length within Ensembl database.
> I try to sum exon's length:
>
> SELECT tp.stable_id, SUM( e.seq_region_end ) - SUM( e.seq_region_start )
> FROM gene g
> JOIN transcript tp ON ( g.gene_id = tp.gene_id )
> JOIN exon_transcript et ON ( et.transcript_id = tp.transcript_id )
> JOIN exon e ON ( e.exon_id = et.exon_id )
> WHERE g.stable_id = 'ENSG00000089234'
> GROUP BY tp.stable_id
>
> But the result is inconsistent with Ensembl official data:
> http://asia.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000089234;r=12:112080797-112123790
>
> If you know how to dig out the datas of 
> variation,orthologue,paralogue,regulation. please also tell me.
>
>
> Thanks million
> -- 
> Gang Chen
> TILSI
> Taicang Institute For Life Science Information
> Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province, 
> P.R.China
> Phone: (+86)512-82782588
>
>
>
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-- 
Jay Humphrey                   Ensembl Genomes Web Developer
EMBL-EBI                       Tel: +44-(0)1223-492682
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/

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