cDNA as Subseq of genomic DNA: intron-exon jcns

Doug Smith dsmith at UCSD.EDU
Mon Aug 23 13:11:31 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" ??? ???
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



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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