1# GTF entries for FBgn0031208, for testing.  Specifically written to have the
2# same isoform model as the same gene in the test GFF file.
3#
4#
5# Simplified model (-- is UTR; == is CDS; .. is intron)
6#
7# -------===============...................=============---------- FBtr0300689
8# -------===============...................========........===---- FBtr0300690
9#
10#
11# ^^^^^^^^^^^^^^^^^^^^exon                 ^^^^^^^^^^^^^^^^^^^^^^^ exon  <-|
12#        =============CDS                  =============CDS                |
13#        * start codon                                  * stop codon
14#
15# ^^^^^^^^^^^^^^^^^^^^exon                 ^^^^^^^^exon    ^^^^^^^exon   <-|
16#                                          ========CDS     ===CDS          | FBtr0300690
17#
18#
19# ======||||||||||||||----||||||||||||-----||||||||||||||========== FBtr0300690
20# ======||||||||||||||----||||||||||||||=========================== FBtr0300689
21#
22#
23# start_codons not listed in GFF
24# ======||||||||||||||----||||||||||||-----||||||||||||||========== FBtr0300690
25# ======||||||||||||||----||||||||||||||=========================== FBtr0300689
26#       ^ start codon shared
27chr2L	protein_coding	start_codon	7680	7682	.	+	0	gene_id "FBgn0031208"; transcript_id "FBtr0300689";
28chr2L	protein_coding	start_codon	7680	7682	.	+	0	gene_id "FBgn0031208"; transcript_id "FBtr0300690";
29#
30# same as unnamed_exon:1 in GFF,but in GTF format, constitutive exons are listed once for each isoform.
31# ======||||||||||||||----||||||||||||-----||||||||||||||========== FBtr0300690
32# ======||||||||||||||----||||||||||||||=========================== FBtr0300689
33# ^------------------^
34#    shared exon between isoforms
35chr2L	protein_coding	exon	7529	8116	.	+	.	gene_id "FBgn0031208"; transcript_id "FBtr0300689";
36chr2L	protein_coding	exon	7529	8116	.	+	.	gene_id "FBgn0031208"; transcript_id "FBtr0300690";
37#
38# same as CDS_FBgn0031208:1_737 in GFF
39#
40# ======||||||||||||||----||||||||||||-----||||||||||||||========== FBtr0300690
41# ======||||||||||||||----||||||||||||||=========================== FBtr0300689
42#       ^------------^
43#       shared CDS between isoforms
44chr2L	protein_coding	CDS	7680	8116	.	+	0	gene_id "FBgn0031208"; transcript_id "FBtr0300689";
45chr2L	protein_coding	CDS	7680	8116	.	+	0	gene_id "FBgn0031208"; transcript_id "FBtr0300690";
46#
47#
48# exon FBgn0031208:3 in GFF -- these two exons imply different-length introns
49# ======||||||||||||||----||||||||||||-----||||||||||||||========== FBtr0300690
50# ======||||||||||||||----||||||||||||||=========================== FBtr0300689
51#                         ^---------------------------------------^
52#                         second of only 2 exons for FBtr*89
53chr2L	protein_coding	exon	8193	9484	.	+	.	gene_id "FBgn0031208"; transcript_id "FBtr0300689";
54#
55# CDS_FBgn0031208:3_737 in GFF
56# ======||||||||||||||----||||||||||||-----||||||||||||||========== FBtr0300690
57# ======||||||||||||||----||||||||||||||=========================== FBtr0300689
58#                         ^------------^
59#                         larger CDS, for 89
60chr2L	protein_coding	CDS	8193	8610	.	+	2	gene_id "FBgn0031208"; transcript_id "FBtr0300689";
61#
62# CDS_FBgn0031208:2_737 in GFF
63# ======||||||||||||||----||||||||||||-----||||||||||||||========== FBtr0300690
64# ======||||||||||||||----||||||||||||||=========================== FBtr0300689
65#                         ^----------^
66#                         smaller CDS, for 90
67chr2L	protein_coding	CDS	8193	8589	.	+	2	gene_id "FBgn0031208"; transcript_id "FBtr0300690";
68#
69# ======||||||||||||||----||||||||||||-----||||||||||||||========== FBtr0300690
70# ======||||||||||||||----||||||||||||||=========================== FBtr0300689
71#                         ^----------^
72#                         smaller exon, for 90
73chr2L	protein_coding	exon	8193	8589	.	+	2	gene_id "FBgn0031208"; transcript_id "FBtr0300690";
74#
75#
76#
77# ======||||||||||||||----||||||||||||-----||||||||||||||========== FBtr0300690
78# ======||||||||||||||----||||||||||||||=========================== FBtr0300689
79#                                          ^----------------------^
80#                                          3rd of 3 exons for FBtr*90
81chr2L	protein_coding	exon	8668	9484	.	+	.	gene_id "FBgn0031208"; transcript_id "FBtr0300690";
82#
83#
84#
85# CDS_FBgn0031208:4_737 in GFF
86# ======||||||||||||||----||||||||||||-----||||||||||||||========== FBtr0300690
87# ======||||||||||||||----||||||||||||||=========================== FBtr0300689
88#                                          ^------------^
89#                                          3rd of 3 CDSs in 90
90chr2L	protein_coding	CDS	8668	9276	.	+	2	gene_id "FBgn0031208"; transcript_id "FBtr0300690";
91#
92# ======||||||||||||||----||||||||||||-----||||||||||||||========== FBtr0300690
93# ======||||||||||||||----||||||||||||||=========================== FBtr0300689
94#                                       ^
95#                                       stop codon for 89
96chr2L	protein_coding	stop_codon	8611	8613	.	+	0	gene_id "FBgn0031208"; transcript_id "FBtr0300689";
97#
98# ======||||||||||||||----||||||||||||-----||||||||||||||========== FBtr0300690
99# ======||||||||||||||----||||||||||||||=========================== FBtr0300689
100#                                                        ^
101#                                                        stop codon for 90
102chr2L	protein_coding	stop_codon	9277	9279	.	+	0	gene_id "FBgn0031208"; transcript_id "FBtr0300690";
103#
104# fake gene 1
105chr2L	FAKE	CDS	10000	11000	.	-	.	gene_id "Fk_gene_1"; transcript_id "transcript_Fk_gene_1";
106chr2L	FAKE	exon	10000	11000	.	-	.	gene_id "Fk_gene_1"; transcript_id "transcript_Fk_gene_1";
107chr2L	FAKE	start_codon	10000	11002	.	-	.	gene_id "Fk_gene_1"; transcript_id "transcript_Fk_gene_1";
108chr2L	FAKE	stop_codon	11001	11003	.	-	.	gene_id "Fk_gene_1"; transcript_id "transcript_Fk_gene_1";
109#
110# fake gene 2, which is non-coding -- say, a snoRNA
111chr2L	FAKE	exon	11500	12500	.	-	.	gene_id "Fk_gene_2"; transcript_id "transcript_Fk_gene_2";
112