[DAS] das track on contigview

[Alex Lam]

Hi developers,
I have an LDAS server serving out transcripts data and a DAS track on our local 
ensembl website (version 8). Transcripts show up correctly except for every 
transcript the first two exons on plus strand or the last 2 exons on minus 
strand rendered as 1 continuous block. So all genes have 1 fewer exon and look 
like as if they have a very long UTR.... :(

I just wonder if anyone has seen this before and knows where the problem lies.

I have attached the xml output from LDAS below. (In this case 169202433 to 
169207936 is just one block, instead of 2 boxes with a hat connector) Any help 
would be greatly appreciated.

Thanks,
Alex


<?xml version="1.0" standalone="yes"?>
<!DOCTYPE DASGFF SYSTEM "http://www.biodas.org/dtd/dasgff.dtd">
<DASGFF>
<GFF version="1.01" 
href="http://tartana/perl/das/dil_transcripts/features?segment=6%3A169200000%2C1
69220000">
<SEGMENT id="6" start="169200000" stop="169220000" version="1.0">
   <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/32" 
label="AL513547.C6.1.3.mRNA">
      <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
      <METHOD id="exon">exon</METHOD>
      <START>169207783</START>
      <END>169207936</END>
      <SCORE>-</SCORE>
      <ORIENTATION>-</ORIENTATION>
      <PHASE>0</PHASE>
      <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
   </FEATURE>
   <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/31" 
label="AL513547.C6.1.3.mRNA">
      <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
      <METHOD id="exon">exon</METHOD>
      <START>169211105</START>
      <END>169211254</END>
      <SCORE>-</SCORE>
      <ORIENTATION>-</ORIENTATION>
      <PHASE>0</PHASE>
      <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
   </FEATURE>
   <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/30" 
label="AL513547.C6.1.3.mRNA">
      <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
      <METHOD id="exon">exon</METHOD>
      <START>169211352</START>
      <END>169211485</END>
      <SCORE>-</SCORE>
      <ORIENTATION>-</ORIENTATION>
      <PHASE>0</PHASE>
      <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
   </FEATURE>
   <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/29" 
label="AL513547.C6.1.3.mRNA">
      <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
      <METHOD id="exon">exon</METHOD>
      <START>169213220</START>
      <END>169213303</END>
      <SCORE>-</SCORE>
      <ORIENTATION>-</ORIENTATION>
      <PHASE>0</PHASE>
      <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
   </FEATURE>
   <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/28" 
label="AL513547.C6.1.3.mRNA">
      <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
      <METHOD id="exon">exon</METHOD>
      <START>169214185</START>
      <END>169214315</END>
      <SCORE>-</SCORE>
      <ORIENTATION>-</ORIENTATION>
      <PHASE>0</PHASE>
      <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
   </FEATURE>
   <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/27" 
label="AL513547.C6.1.3.mRNA">
      <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
      <METHOD id="exon">exon</METHOD>
      <START>169216402</START>
      <END>169216508</END>
      <SCORE>-</SCORE>
      <ORIENTATION>-</ORIENTATION>
      <PHASE>0</PHASE>
      <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
   </FEATURE>
   <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/26" 
label="AL513547.C6.1.3.mRNA">
      <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
      <METHOD id="exon">exon</METHOD>
      <START>169219242</START>
      <END>169219402</END>
      <SCORE>-</SCORE>
      <ORIENTATION>-</ORIENTATION>
      <PHASE>0</PHASE>
      <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
   </FEATURE>
   <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/33" 
label="AL513547.C6.1.3.mRNA">
      <TYPE id="exon:curated" category="transcription">exon:curated</TYPE>
      <METHOD id="exon">exon</METHOD>
      <START>169202433</START>
      <END>169205788</END>
      <SCORE>-</SCORE>
      <ORIENTATION>-</ORIENTATION>
      <PHASE>0</PHASE>
      <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
   </FEATURE>
   <FEATURE id="Transcript:AL513547.C6.1.3.mRNA/25" 
label="AL513547.C6.1.3.mRNA">
      <TYPE id="transcript:curated" 
category="transcription">transcript:curated</TYPE>
      <METHOD id="transcript">transcript</METHOD>
      <START>169202433</START>
      <END>169219402</END>
      <SCORE>-</SCORE>
      <ORIENTATION>-</ORIENTATION>
      <PHASE>0</PHASE>
      <GROUP id="Transcript:AL513547.C6.1.3.mRNA" />
   </FEATURE>

</SEGMENT>
</GFF>
</DASGFF>

----
Alex C. Lam
Computer Associate
JDRF/WT Diabetes and Inflammation Laboratory
Cambridge Institute for Medical Research
Wellcome Trust/MRC Building
University of Cambridge
Hills Road, Cambridge,  CB2 2XY
Great Britain

Office: 01223 763229
Web: http://www-gene.cimr.cam.ac.uk/todd/