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Member "augustus-3.3.3/docs/tutorial-cgp/data/augCGP_rnaseq/pred2/canFam3.cgp.gff" (22 May 2019, 5287 Bytes) of package /linux/misc/augustus-3.3.3.tar.gz:


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    1 # This output was generated with AUGUSTUS (version 3.3.1).
    2 # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
    3 # O. Keller, S. K├Ânig, L. Gerischer, L. Romoth and Katharina Hoff.
    4 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
    5 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
    6 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
    7 #
    8 #----- prediction for species 'canFam3' -----
    9 #
   10 #----- prediction on sequence range chr6:42771-93097 (50327bp) -----
   11 #
   12 # start gene g2
   13 chr6	AUGUSTUS	gene	55420	91634	.	+	.	g2
   14 chr6	AUGUSTUS	transcript	55420	91634	.	+	.	g2.t1
   15 chr6	AUGUSTUS	start_codon	55420	55422	.	+	0	transcript_id "g2.t1"; gene_id "g2";
   16 chr6	AUGUSTUS	CDS	55420	55538	0.46	+	0	transcript_id "g2.t1"; gene_id "g2";
   17 chr6	AUGUSTUS	exon	55420	55538	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   18 chr6	AUGUSTUS	CDS	67472	67612	0.98	+	1	transcript_id "g2.t1"; gene_id "g2";
   19 chr6	AUGUSTUS	exon	67472	67612	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   20 chr6	AUGUSTUS	CDS	71165	71261	0.83	+	1	transcript_id "g2.t1"; gene_id "g2";
   21 chr6	AUGUSTUS	exon	71165	71261	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   22 chr6	AUGUSTUS	CDS	77034	77103	0.27	+	0	transcript_id "g2.t1"; gene_id "g2";
   23 chr6	AUGUSTUS	exon	77034	77103	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   24 chr6	AUGUSTUS	CDS	78429	78505	0.89	+	2	transcript_id "g2.t1"; gene_id "g2";
   25 chr6	AUGUSTUS	exon	78429	78505	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   26 chr6	AUGUSTUS	CDS	79014	79151	0.99	+	0	transcript_id "g2.t1"; gene_id "g2";
   27 chr6	AUGUSTUS	exon	79014	79151	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   28 chr6	AUGUSTUS	CDS	82780	83309	1	+	0	transcript_id "g2.t1"; gene_id "g2";
   29 chr6	AUGUSTUS	exon	82780	83309	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   30 chr6	AUGUSTUS	CDS	84005	84175	0.97	+	1	transcript_id "g2.t1"; gene_id "g2";
   31 chr6	AUGUSTUS	exon	84005	84175	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   32 chr6	AUGUSTUS	CDS	86687	86932	0.99	+	1	transcript_id "g2.t1"; gene_id "g2";
   33 chr6	AUGUSTUS	exon	86687	86932	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   34 chr6	AUGUSTUS	CDS	88713	88820	0.86	+	1	transcript_id "g2.t1"; gene_id "g2";
   35 chr6	AUGUSTUS	exon	88713	88820	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   36 chr6	AUGUSTUS	CDS	90322	90489	1	+	1	transcript_id "g2.t1"; gene_id "g2";
   37 chr6	AUGUSTUS	exon	90322	90489	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   38 chr6	AUGUSTUS	CDS	90920	91046	1	+	1	transcript_id "g2.t1"; gene_id "g2";
   39 chr6	AUGUSTUS	exon	90920	91634	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   40 chr6	AUGUSTUS	stop_codon	91044	91046	.	+	0	transcript_id "g2.t1"; gene_id "g2";
   41 chr6	AUGUSTUS	tts	91634	91634	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   42 # protein sequence = [MGESSGLAAPLRLDLDPHSLPLMKSKCGKGAGRRCEVLCTCGSWREPVHPYYVSSGYALAPATSANDSEQQSLSSDAD
   43 # SLSLTDSSVDGIPPYRIRKQHRREMQESVQVNGRVPLPHIPKVHGFNDSLFLGDFPVPLQLEGTEQSRIPSLVWALGGCCPVLRRAVLQARTYRMPKE
   44 # IRVEPQKFAAELIHRLEAIQRTREAEEKLEERLKRVRMEEEGEDGDVPSGPLGAIHKLPLAPAWHHFPPRYADVGCVGLRDAHEENPESILDEHVQRV
   45 # MRTPGCQSPGPGHRSPDNAHVPKIVGVLGGVPSGHGKHAPKSGAKLDTAGPHLHRHSHHHSHHSAARPKEQADAEAARRVQGSFAWGPELHGHTAKPR
   46 # SHSESVGAAPNASDSLAYSGKAGTASRRNAKKAESGKNASTEVPGPSEDTDKNQKIMQWIIEGEKEISRHRKAGHGSSGAKKQQVHESSRPLSVERPG
   47 # AVHPWVSAQLRNSVQPSHLFIQDPTMPPNPAPNPLTQLEEARRRLEEEEKRASKLPSKQRYVQEVIQRGRSCIRPTCTPVLSVVPAVSDLELSETETK
   48 # SQRKAGSGSAQPCDSIVVAYYFCGEPIPYRTLVRGRAVTLGQFKELLTKKGNYRYYFKKVSDEFDCGVVFEEVREDEAVLPVFEEKIIGKVEKVD]
   49 # Evidence for and against this transcript:
   50 # % of transcript supported by hints (any source): 0
   51 # CDS exons: 0/12
   52 # CDS introns: 0/11
   53 # 5'UTR exons and introns: 0/0
   54 # 3'UTR exons and introns: 0/1
   55 # hint groups fully obeyed: 39
   56 #     RM:  39 
   57 # incompatible hint groups: 0
   58 # end gene g2
   59 ###
   60 # start gene g1
   61 chr6	AUGUSTUS	gene	91857	93075	.	-	.	g1
   62 chr6	AUGUSTUS	transcript	91857	93075	.	-	.	g1.t1
   63 chr6	AUGUSTUS	tts	91857	91857	.	-	.	transcript_id "g1.t1"; gene_id "g1";
   64 chr6	AUGUSTUS	exon	91857	92007	.	-	.	transcript_id "g1.t1"; gene_id "g1";
   65 chr6	AUGUSTUS	stop_codon	91963	91965	.	-	0	transcript_id "g1.t1"; gene_id "g1";
   66 chr6	AUGUSTUS	CDS	91963	92007	0.29	-	0	transcript_id "g1.t1"; gene_id "g1";
   67 chr6	AUGUSTUS	CDS	92113	92223	0.24	-	0	transcript_id "g1.t1"; gene_id "g1";
   68 chr6	AUGUSTUS	exon	92113	92223	.	-	.	transcript_id "g1.t1"; gene_id "g1";
   69 chr6	AUGUSTUS	CDS	92393	92574	1	-	2	transcript_id "g1.t1"; gene_id "g1";
   70 chr6	AUGUSTUS	exon	92393	92574	.	-	.	transcript_id "g1.t1"; gene_id "g1";
   71 chr6	AUGUSTUS	CDS	92765	92885	1	-	0	transcript_id "g1.t1"; gene_id "g1";
   72 chr6	AUGUSTUS	exon	92765	92885	.	-	.	transcript_id "g1.t1"; gene_id "g1";
   73 chr6	AUGUSTUS	CDS	92977	93075	0.97	-	0	transcript_id "g1.t1"; gene_id "g1";
   74 chr6	AUGUSTUS	exon	92977	93075	.	-	.	transcript_id "g1.t1"; gene_id "g1";
   75 chr6	AUGUSTUS	start_codon	93073	93075	.	-	0	transcript_id "g1.t1"; gene_id "g1";
   76 # protein sequence = [METTKKYAPVGGGPLTAAAVATFCHAVLSGQVKPYLLSQDVPPDWDRRPVKTLVGKNFEQVAFDETKNVFVKFYAPWC
   77 # THCKAMAAAWEALAEKYKDHEDIVIAELDATANELEAFPVHGFPTLKYFPAGPGRKVIEYKSTRDVETFSKFLDNGGELPAEEPTEEPTAPFPDTPAN
   78 # ASAEPKEEL]
   79 # Evidence for and against this transcript:
   80 # % of transcript supported by hints (any source): 0
   81 # CDS exons: 0/5
   82 # CDS introns: 0/4
   83 # 5'UTR exons and introns: 0/0
   84 # 3'UTR exons and introns: 0/1
   85 # hint groups fully obeyed: 2
   86 #     RM:   2 
   87 # incompatible hint groups: 0
   88 # end gene g1
   89 ###