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