53 lines
No EOL
1.8 KiB
HTML
53 lines
No EOL
1.8 KiB
HTML
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<title>Spliced-seg</title>
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<h3>Spliced-seg</h3><pre>Defined in file <a href="seqalign.asn.html">seqalign.asn</a>
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C++ class: <a href="../doxyhtml/classCSpliced__seg.html">CSpliced_seg</a>
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Spliced-seg ::= SEQUENCE {
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-- product is either protein or transcript (cDNA)
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product-id <a href="Seq-id.html">Seq-id</a> OPTIONAL,
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genomic-id <a href="Seq-id.html">Seq-id</a> OPTIONAL,
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-- should be 'plus' or 'minus'
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product-strand <a href="Na-strand.html">Na-strand</a> OPTIONAL ,
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genomic-strand <a href="Na-strand.html">Na-strand</a> OPTIONAL ,
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product-type ENUMERATED {
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transcript(0),
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protein(1)
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},
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-- set of segments involved
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-- each segment corresponds to one exon
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-- exons are always in biological order
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exons SEQUENCE OF <a href="Spliced-exon.html">Spliced-exon</a> ,
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-- start of poly(A) tail on the transcript
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-- For sense transcripts:
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-- aligned product positions < poly-a <= product-length
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-- poly-a == product-length indicates inferred poly(A) tail at transcript's end
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-- For antisense transcripts:
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-- -1 <= poly-a < aligned product positions
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-- poly-a == -1 indicates inferred poly(A) tail at transcript's start
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poly-a INTEGER OPTIONAL,
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-- length of the product, in bases/residues
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-- from this (or from poly-a if present), a 3' unaligned length can be extracted
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product-length INTEGER OPTIONAL,
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-- alignment descriptors / modifiers
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-- this provides us a set for extension
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modifiers SET OF <a href="Spliced-seg-modifier.html">Spliced-seg-modifier</a> OPTIONAL
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}</pre>
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