cDNA as Subseq of genomic DNA: intron-exon jcns

Mike Cherry cherry at GENOME.STANFORD.EDU
Mon Aug 23 14:53:55 EST 1999


> 
> Could someone suggest how to handle the following in a .ace file?
> 
> I have a cDNA that overlaps an exon-intron boundary of a genomic
> sequence, and wish to encode the cDNA as a Subsequence of the
> genomic.
> 
> How do I handle the cDNA coordinates to get proper graphic display
> of the sequences?
> 
> 
> 
> Example:
> 
> Sequence : "Genomic_Seq"
> DNA      "Genomic_Seq" 1000
> Subsequence      "cDNA_Seq" ??? ???

Subsequence      "cDNA_Seq" 200 800

> exon     200 300 "" Location "200..300"
> exon     450 800 "" Location "450..800"
> Intron   301 449 "" Location "301..449"
> 
> Sequence : "cDNA_Seq"
> DNA      "cDNA_Seq" 500
Source	 "Genomic_Seq"
Source_Exon	 1 101
Source_Exon	 251 601

The Source_Exon tags will define the association with the Source
sequence.  If the two sequences do not match you will see a warning on
the sequence display.  I have not tried this but I think it should
work.

Mike


> 
> 
> 
> The 500 bp of the cDNA overlap the genomic DNA from
> 100-300 and from 450-750 (intro-exon junction in the
> cDNA is between nucs 200 and 201)
> 
> I appreciate any suggestions ...
> Thanks
>   -Doug
> 
> Doug Smith, Professor of Biology .... dsmith at ucsd.edu
> Department of Biology, 0116; UCSD; La Jolla CA  92093
> phone:  858-534-2620                FAX: 858-534-7108
> NOTE the area code: 619 changed to 858 in June, 1999!
> http://www-biology.ucsd.edu/others/dsmith/dnasys.html
> 
> 
> 





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