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