[ensembl-dev] Ensembl release 65 is out !

[Karyn Megy]

Dear Hiram, 

Drosophila has some strange bits of biology - one if it is this gene (mod(mdg4), FBgn0002781): lots of alternative transcripts, and some exons on the opposite strand.   

See the Ensembl genome browser: 
http://www.ensembl.org/Drosophila_melanogaster/Location/View?g=FBgn0002781;r=3R:17177331-17203121

We import the Drosophila data from FlyBase - see their site for this transcript: 
http://flybase.org/reports/FBtr0084077.html


Best,
Karyn.


On 15 Dec 2011, at 22:00, Hiram Clawson wrote:

> Good Afternoon Ensembl Fans:
> 
> I'm having some difficulty processing the GTF file:
> 
>    Drosophila_melanogaster.BDGP5.25.65.gtf.gz
> 
> It appears to have gene elements defined in illegal locations.
> 
> For example: gene_id "FBgn0002781"; transcript_id "FBtr0084077";
> 
> Note the strand indication for exon_number "2" is + and the other exons are -
> 
> 3R protein_coding exon 17202324 17202463 . - .  gene_id "FBgn0002781"; transcript_id "FBtr0084077"; exon_number "1"; gene_name "mod(mdg4)"; transcript_name "mod(mdg4)-RR"; seqedit "false";
> 3R protein_coding exon 17177331 17177608 . + .  gene_id "FBgn0002781"; transcript_id "FBtr0084077"; exon_number "2"; gene_name "mod(mdg4)"; transcript_name "mod(mdg4)-RR"; seqedit "false";
> 3R protein_coding exon 17203010 17203121 . - .  gene_id "FBgn0002781"; transcript_id "FBtr0084077"; exon_number "3"; gene_name "mod(mdg4)"; transcript_name "mod(mdg4)-RR"; seqedit "false";
> 3R protein_coding exon 17202541 17202798 . - .  gene_id "FBgn0002781"; transcript_id "FBtr0084077"; exon_number "4"; gene_name "mod(mdg4)"; transcript_name "mod(mdg4)-RR"; seqedit "false";
> 3R protein_coding start_codon 17202752 17202754 . - 0  gene_id "FBgn0002781"; transcript_id "FBtr0084077"; exon_number "4"; gene_name "mod(mdg4)"; transcript_name "mod(mdg4)-RR";
> 3R protein_coding exon 17200782 17201634 . - .  gene_id "FBgn0002781"; transcript_id "FBtr0084077"; exon_number "5"; gene_name "mod(mdg4)"; transcript_name "mod(mdg4)-RR"; seqedit "false";
> 
> Is there something I'm missing here ?
> 
> --Hiram
> 
> 
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