# Reference: http://mblab.wustl.edu/GTF22.html#examples
# Here is an example of a gene on the negative strand including UTR regions. Larger coordinates are 5' of smaller
# coordinates. Thus, the start codon is 3 bp with largest coordinates among all those bp that fall within the CDS
# regions. Note that the stop codon lies between the 3UTR and the CDS
#
1	Twinscan	inter	5141	8522	.	-	.	gene_id ""; transcript_id "";
1	Twinscan	inter_CNS	8523	9711	.	-	.	gene_id ""; transcript_id "";
1	Twinscan	inter	9712	13182	.	-	.	gene_id ""; transcript_id "";
# Note the split start codon. The second start codon region has a frame of 2, since it is the second base, and has
# an accompanying CDS feature, since CDS always includes the start codon.
#
1	Twinscan	3UTR	65149	65487	.	-	.	gene_id "140.000"; transcript_id "140.000.1";
1	Twinscan	3UTR	66823	66992	.	-	.	gene_id "140.000"; transcript_id "140.000.1";
1	Twinscan	stop_codon	66993	66995	.	-	0	gene_id "140.000"; transcript_id "140.000.1";
1	Twinscan	CDS	66996	66999	.	-	1	gene_id "140.000"; transcript_id "140.000.1";
1	Twinscan	intron_CNS	70103	70151	.	-	.	gene_id "140.000"; transcript_id "140.000.1";
1	Twinscan	CDS	70207	70294	.	-	2	gene_id "140.000"; transcript_id "140.000.1";
1	Twinscan	CDS	71696	71807	.	-	0	gene_id "140.000"; transcript_id "140.000.1";
1	Twinscan	start_codon	71805	71806	.	-	0	gene_id "140.000"; transcript_id "140.000.1";
1	Twinscan	start_codon	73222	73222	.	-	2	gene_id "140.000"; transcript_id "140.000.1";
1	Twinscan	CDS	73222	73222	.	-	0	gene_id "140.000"; transcript_id "140.000.1";
1	Twinscan	5UTR	73223	73504	.	-	.	gene_id "140.000"; transcript_id "140.000.1";
#
# Here is an example in which the "exon" feature is used. It is a 5 exon gene with 3 translated exons.
#
1	Twinscan	exon	150	200	.	+	.	gene_id "381.000"; transcript_id "381.000.1"; 
1	Twinscan	exon	300	401	.	+	.	gene_id "381.000"; transcript_id "381.000.1"; 
1	Twinscan	CDS	380	401	.	+	0	gene_id "381.000"; transcript_id "381.000.1"; 
1	Twinscan	exon	501	650	.	+	.	gene_id "381.000"; transcript_id "381.000.1"; 
1	Twinscan	CDS	501	650	.	+	2	gene_id "381.000"; transcript_id "381.000.1"; 
1	Twinscan	exon	700	800	.	+	.	gene_id "381.000"; transcript_id "381.000.1"; 
1	Twinscan	CDS	700	707	.	+	2	gene_id "381.000"; transcript_id "381.000.1"; 
1	Twinscan	exon	900	1000	.	+	.	gene_id "381.000"; transcript_id "381.000.1"; 
1	Twinscan	start_codon	380	382	.	+	0	gene_id "381.000"; transcript_id "381.000.1"; 
1	Twinscan	stop_codon	708	710	.	+	0	gene_id "381.000"; transcript_id "381.000.1";