1# GFF entries for FBgn0031208, for testing.
2#
3# This is the first gene in FlyBase r5.23, and entries contain the full gene
4# model.  To be able to understand, debug, and write tests, below are 1) a
5# simple graphical representation, and then 2) the explicit features defined by
6# the GFF.
7#
8# Simplified model (-- is UTR; == is CDS; .. is intron)
9#
10# -------===============...................=============---------- FBtr0300689
11# -------===============...................========........===---- FBtr0300690
12#
13#
14# Full model, including all features described below.  Note that exons contain
15# UTRs and that:
16#    5'UTR + first CDS = first exon
17#    3'UTR + last CDS = last exon
18#    middle exons = middle CDSs
19#
20# |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| gene
21#
22#
23#
24# ^^^^^^^^^^^^^^^^^^^^exon                 ^^^^^^^^^^^^^^^^^^^^^^^ exon  <-|
25# -------5'UTR                                          ----------3'UTR    | FBtr0300689
26#         =============CDS                 =============CDS                |
27#                      ....................intron                        <-|
28#
29#
30#
31#
32# ^^^^^^^^^^^^^^^^^^^^exon                 ^^^^^^^^exon    ^^^^^^^exon   <-|
33#                                                             ----3'UTR    |
34#                                          ========CDS     ===CDS          | FBtr0300690
35#                      ....................intron                          |
36#                                                  ........intron        <-|
37#
38#         ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,protein
39#         ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,protein
40#                                             /////PCR product
41#
42#
43# A fake gene, on the opposite strand and starting 800 bp or so downstream.
44#
45# ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  Fk_gene_1
46# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  Fk_gene_1:1 (exon)
47# ============================================================  CDS:Fk_gene_1
48# ------------------------------------------------------------  transcript_Fk_gene_1
49#
50#
51# Note that the ID for the first exon has been removed for testing the
52# automatic ID creation.  In the database, this should come up as
53# "unnamed_exon_1".
54#
55chr2L	FlyBase	gene	7529	9484	.	+	.	ID=FBgn0031208;Name=CG11023;Ontology_term=SO:0000010,SO:0000087,GO:0008234,GO:0006508;Dbxref=FlyBase:FBan0011023,FlyBase_Annotation_IDs:CG11023,GB:AE003590,GB_protein:AAO41164,GB:AI944728,GB:AJ564667,GB_protein:CAD92822,GB:BF495604,UniProt/TrEMBL:Q6KEV3,UniProt/TrEMBL:Q86BM6,INTERPRO:IPR003653,BIOGRID:59420,dedb:5870,GenomeRNAi_gene:33155,ihop:59383;derived_computed_cyto=21A5-21A5;gbunit=AE014134
56chr2L	FlyBase	mRNA	7529	9484	.	+	.	ID=FBtr0300689;Name=CG11023-RB;Parent=FBgn0031208;Dbxref=FlyBase_Annotation_IDs:CG11023-RB;score_text=Strongly Supported;score=11
57chr2L	FlyBase	mRNA	7529	9484	.	+	.	ID=FBtr0300690;Name=CG11023-RC;Parent=FBgn0031208;Dbxref=FlyBase_Annotation_IDs:CG11023-RC;score_text=Moderately Supported;score=7
58
59# ID for the first exon has been removed for testing IDs using Name instead of
60# ID, and the second exon has neither ID nor Name, for testing auto-ID
61# creation.
62chr2L	FlyBase	five_prime_UTR	7529	7679	.	+	.	ID=five_prime_UTR_FBgn0031208:1_737;Name=CG11023-u5;Parent=FBtr0300689,FBtr0300690
63chr2L	FlyBase	exon	7529	8116	.	+	.	Name=CG11023:1;Parent=FBtr0300689,FBtr0300690
64chr2L	FlyBase	CDS	7680	8116	.	+	0	ID=CDS_FBgn0031208:1_737;Name=CG11023-cds;Parent=FBtr0300689,FBtr0300690
65chr2L	FlyBase	intron	8117	8192	.	+	.	ID=intron_FBgn0031208:1_FBgn0031208:2;Name=CG11023-in;Parent=FBtr0300690
66chr2L	FlyBase	intron	8117	8192	.	+	.	ID=intron_FBgn0031208:1_FBgn0031208:3;Name=CG11023-in;Parent=FBtr0300689
67chr2L	FlyBase	exon	8193	8589	.	+	.	Parent=FBtr0300690
68chr2L	FlyBase	exon	8193	9484	.	+	.	ID=FBgn0031208:3;Name=CG11023:3;Parent=FBtr0300689
69chr2L	FlyBase	CDS	8193	8610	.	+	2	ID=CDS_FBgn0031208:3_737;Name=CG11023-cds;Parent=FBtr0300689
70chr2L	FlyBase	CDS	8193	8589	.	+	2	ID=CDS_FBgn0031208:2_737;Name=CG11023-cds;Parent=FBtr0300690
71chr2L	FlyBase	exon	8668	9484	.	+	.	ID=FBgn0031208:4;Name=CG11023:4;Parent=FBtr0300690
72chr2L	FlyBase	CDS	8668	9276	.	+	0	ID=CDS_FBgn0031208:4_737;Name=CG11023-cds;Parent=FBtr0300690
73chr2L	FlyBase	intron	8590	8667	.	+	.	ID=intron_FBgn0031208:2_FBgn0031208:4;Name=CG11023-in;Parent=FBtr0300690
74chr2L	FlyBase	three_prime_UTR	8611	9484	.	+	.	ID=three_prime_UTR_FBgn0031208:3_737;Name=CG11023-u3;Parent=FBtr0300689
75chr2L	FlyBase	three_prime_UTR	9277	9484	.	+	.	ID=three_prime_UTR_FBgn0031208:4_737;Name=CG11023-u3;Parent=FBtr0300690
76chr2L	FlyBase	protein	7680	9273	.	+	.	ID=FBpp0289914;Name=CG11023-PC;Derives_from=FBtr0300690;Dbxref=FlyBase_Annotation_IDs:CG11023-PC;derived_isoelectric_point=7.15;derived_molecular_weight=55247.1
77chr2L	FlyBase	protein	7680	8607	.	+	.	ID=FBpp0289913;Name=CG11023-PB;Derives_from=FBtr0300689;Dbxref=FlyBase_Annotation_IDs:CG11023-PB;derived_isoelectric_point=6.96;derived_molecular_weight=32613.1
78chr2L	DGRC_1	pcr_product	8272	8589	.	+	.	ID=INC121G01_pcr_product;Name=INC121G01;Dbxref=DGRC-1:INC121G01
79
80# Fake gene, on the opposite strand. Useful for testing proximity routines.
81chr2L	FAKE	gene	10000	11000	.	-	.	ID=Fk_gene_1;
82chr2L	FAKE	mRNA	10000	11000	.	-	.	ID=transcript_Fk_gene_1;Parent=Fk_gene_1;
83chr2L	FAKE	exon	10000	11000	.	-	.	ID=Fk_gene_1:1;Parent=transcript_Fk_gene_1;
84chr2L	FAKE	CDS	10000	11000	.	-	.	ID=CDS:Fk_gene_1:1; Parent=transcript_Fk_gene_1
85#
86# Another fake gene, used for promoter truncation tests.  This one is non-coding.
87chr2L	FAKE	gene	11500	12500	.	-	.	ID=Fk_gene_2
88chr2L	FAKE	mRNA	11500	12500	.	-	.	ID=transcript_Fk_gene_2;Parent=Fk_gene_2
89chr2L	FAKE	exon	11500	12500	.	+	.	ID=Fk_gene_2:1;Parent=transcript_Fk_gene_2
90>chr2L
91AAATAGTGATGCTAGCTAGCTAGCTCGTACGATCGTCGATCGATCGATCGTACGATCGATCCGCGCGCGCGCGCGATATATAGCTTGATGCTGATGTCTGACGACACTG
92ACTGACTGCCGCTAGCGCGTATCGCGCGCGCATCGTACGCTGCTACGTCGATCGCGCGCGCTATAGCTACGTCGATCGATCGTAGCTAGCTAGCTAGCTACGCGCGCGC
93