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#
#Protein-Coding Genes
#
#We'll now look at how to represent several common cases, starting
#with protein-coding genes.
#
#The most general way of representing a protein-coding gene is the
#so-called "three-level gene." The top level is a feature of type
#"gene" which bundles up the gene's transcripts and regulatory
#elements. Beneath this level are one or more transcripts of type
#"mRNA". This level can also accommodate promoters and other
#cis-regulatory elements. At the third level are the components of the
#mRNA transcripts, most commonly CDS coding segments and UTRs. This
#example shows how to represent a gene named "EDEN" which has three
#alternatively-spliced mRNA transcripts:
ctg123 example gene 1050 9000 . + . ID=EDEN;Name=EDEN;Note=protein kinase
ctg123 example mRNA 1050 9000 . + . ID=EDEN.1;Parent=EDEN;Name=EDEN.1;Index=1
ctg123 example five_prime_UTR 1050 1200 . + . Parent=EDEN.1
ctg123 example CDS 1201 1500 . + 0 Parent=EDEN.1
ctg123 example CDS 3000 3902 . + 0 Parent=EDEN.1
ctg123 example CDS 5000 5500 . + 0 Parent=EDEN.1
ctg123 example CDS 7000 7608 . + 0 Parent=EDEN.1
ctg123 example three_prime_UTR 7609 9000 . + . Parent=EDEN.1
ctg123 example mRNA 1050 9000 . + . ID=EDEN.2;Parent=EDEN;Name=EDEN.2;Index=1
ctg123 example five_prime_UTR 1050 1200 . + . Parent=EDEN.2
ctg123 example CDS 1201 1500 . + 0 Parent=EDEN.2
ctg123 example CDS 5000 5500 . + 0 Parent=EDEN.2
ctg123 example CDS 7000 7608 . + 0 Parent=EDEN.2
ctg123 example three_prime_UTR 7609 9000 . + . Parent=EDEN.2
ctg123 example mRNA 1300 9000 . + . ID=EDEN.3;Parent=EDEN;Name=EDEN.3;Index=1
ctg123 example five_prime_UTR 1300 1500 . + . Parent=EDEN.3
ctg123 example five_prime_UTR 3000 3300 . + . Parent=EDEN.3
ctg123 example CDS 3301 3902 . + 0 Parent=EDEN.3
ctg123 example CDS 5000 5500 . + 1 Parent=EDEN.3
ctg123 example CDS 7000 7600 . + 1 Parent=EDEN.3
ctg123 example three_prime_UTR 7601 9000 . + . Parent=EDEN.3
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