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Member "augustus-3.3.3/docs/tutorial-cgp/data/augCGP_rnaseq/pred5/mm10.cgp.gff" (22 May 2019, 5804 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 'mm10' -----
    9 #
   10 #----- prediction on sequence range chr17:1-26955 (26955bp) -----
   11 #
   12 # start gene g2
   13 chr17	AUGUSTUS	gene	7905	17296	.	+	.	g2
   14 chr17	AUGUSTUS	transcript	7905	17296	.	+	.	g2.t1
   15 chr17	AUGUSTUS	exon	7905	8629	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   16 chr17	AUGUSTUS	start_codon	8512	8514	.	+	0	transcript_id "g2.t1"; gene_id "g2";
   17 chr17	AUGUSTUS	CDS	8512	8629	1	+	0	transcript_id "g2.t1"; gene_id "g2";
   18 chr17	AUGUSTUS	CDS	11821	11995	1	+	2	transcript_id "g2.t1"; gene_id "g2";
   19 chr17	AUGUSTUS	exon	11821	11995	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   20 chr17	AUGUSTUS	CDS	12081	12288	1	+	1	transcript_id "g2.t1"; gene_id "g2";
   21 chr17	AUGUSTUS	exon	12081	12288	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   22 chr17	AUGUSTUS	CDS	12473	12600	1	+	0	transcript_id "g2.t1"; gene_id "g2";
   23 chr17	AUGUSTUS	exon	12473	12600	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   24 chr17	AUGUSTUS	CDS	12801	13069	1	+	1	transcript_id "g2.t1"; gene_id "g2";
   25 chr17	AUGUSTUS	exon	12801	13069	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   26 chr17	AUGUSTUS	CDS	13172	13491	1	+	2	transcript_id "g2.t1"; gene_id "g2";
   27 chr17	AUGUSTUS	exon	13172	13491	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   28 chr17	AUGUSTUS	CDS	13924	14014	1	+	0	transcript_id "g2.t1"; gene_id "g2";
   29 chr17	AUGUSTUS	exon	13924	14014	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   30 chr17	AUGUSTUS	CDS	14095	14218	1	+	2	transcript_id "g2.t1"; gene_id "g2";
   31 chr17	AUGUSTUS	exon	14095	14218	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   32 chr17	AUGUSTUS	CDS	14461	14597	1	+	1	transcript_id "g2.t1"; gene_id "g2";
   33 chr17	AUGUSTUS	exon	14461	14597	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   34 chr17	AUGUSTUS	CDS	15346	15524	1	+	2	transcript_id "g2.t1"; gene_id "g2";
   35 chr17	AUGUSTUS	exon	15346	15524	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   36 chr17	AUGUSTUS	CDS	15601	15747	1	+	0	transcript_id "g2.t1"; gene_id "g2";
   37 chr17	AUGUSTUS	exon	15601	15747	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   38 chr17	AUGUSTUS	CDS	16602	16718	1	+	0	transcript_id "g2.t1"; gene_id "g2";
   39 chr17	AUGUSTUS	exon	16602	16718	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   40 chr17	AUGUSTUS	CDS	17000	17296	1	+	0	transcript_id "g2.t1"; gene_id "g2";
   41 chr17	AUGUSTUS	exon	17000	17296	.	+	.	transcript_id "g2.t1"; gene_id "g2";
   42 chr17	AUGUSTUS	stop_codon	17294	17296	.	+	0	transcript_id "g2.t1"; gene_id "g2";
   43 # protein sequence = [MGRVGAGGTAREAATGSLLLLLLLLARPPPAAASNSKESEAGLVSEHFSQAPQKLSFYSWYGSTRLFHFRVPPDTVLL
   44 # RWLLHVSQGSPSCTDEEITVHFRYGAPPVINPLGTSFPDNTLSHASFHIRALLSTLMLDNTSVNISHPAPGDWFLVAHLPPSSQKIQVKGFVPTCAYI
   45 # FQPDMLVMRVVEVSTLEPDVPLPQTLLSYPSYLKIFVPEYTQELRLELQGCVSSVSPGCPVRVTVGATTLPRNFQRVLTCTGLAPSCHLLLSSPPWGR
   46 # WLQVTFESLAEPHVTVGFTAKAVFTVCRPWSVTIHHLIQNNPNQTYDTSAIQLSQSAVHRDLGRSSRVDSGPFCLLNYPVLREDTDVVSVHFQPLNGA
   47 # FVLVHSSMPSVMQLRLDTGMDSGGSFIIVLRTNKTEVTNGTLVAACVNAASPFLSFNTSLNCTTAFFQGYPMFLRASSHMANLIMPFPETDNWYLSLQ
   48 # LVCPESPEDCEQAVVRVETILYLVPCLNDCGPYGQCLLLRRYGYVYAGCSCKAGWRGWSCTDNSTAQTVAQQRAAALLLTLSNLMFLAPIAISLHRSF
   49 # LVEASVYFYTMFFSTFYHACDQPGEAVLCILSYDTLQYCDFLGSGASTWVTILCMARLKTILKQVLLVLGTLVIAMSLQMDRRGIWNLMGPCVFAFVI
   50 # MASMWIYRCGHRGQCYPTSWQRWVFYLLPGISMASVGIAMYTSMMTSDNYYYTHSIWHILLAGSAAFLLPPREEKAGSWACLQKFPCHYQICRNDRDE
   51 # LYTVT]
   52 # Evidence for and against this transcript:
   53 # % of transcript supported by hints (any source): 100
   54 # CDS exons: 13/13
   55 #      W:  13 
   56 # CDS introns: 12/12
   57 #      E:  12 
   58 # 5'UTR exons and introns: 1/1
   59 #      W:   1 
   60 # 3'UTR exons and introns: 0/0
   61 # hint groups fully obeyed: 83
   62 #      E:  12 
   63 #      W:  71 
   64 # incompatible hint groups: 269
   65 #      E:   1 
   66 #      W: 268 
   67 # end gene g2
   68 ###
   69 # start gene g1
   70 chr17	AUGUSTUS	gene	18581	21677	.	+	.	g1
   71 chr17	AUGUSTUS	transcript	18581	21677	.	+	.	g1.t1
   72 chr17	AUGUSTUS	tss	18581	18581	.	+	.	transcript_id "g1.t1"; gene_id "g1";
   73 chr17	AUGUSTUS	exon	18581	18911	.	+	.	transcript_id "g1.t1"; gene_id "g1";
   74 chr17	AUGUSTUS	start_codon	18624	18626	.	+	0	transcript_id "g1.t1"; gene_id "g1";
   75 chr17	AUGUSTUS	CDS	18624	18911	1	+	0	transcript_id "g1.t1"; gene_id "g1";
   76 chr17	AUGUSTUS	CDS	19618	19770	1	+	0	transcript_id "g1.t1"; gene_id "g1";
   77 chr17	AUGUSTUS	exon	19618	19770	.	+	.	transcript_id "g1.t1"; gene_id "g1";
   78 chr17	AUGUSTUS	CDS	20319	20453	1	+	0	transcript_id "g1.t1"; gene_id "g1";
   79 chr17	AUGUSTUS	exon	20319	20453	.	+	.	transcript_id "g1.t1"; gene_id "g1";
   80 chr17	AUGUSTUS	CDS	20540	20626	1	+	0	transcript_id "g1.t1"; gene_id "g1";
   81 chr17	AUGUSTUS	exon	20540	20626	.	+	.	transcript_id "g1.t1"; gene_id "g1";
   82 chr17	AUGUSTUS	CDS	21333	21443	1	+	0	transcript_id "g1.t1"; gene_id "g1";
   83 chr17	AUGUSTUS	exon	21333	21677	.	+	.	transcript_id "g1.t1"; gene_id "g1";
   84 chr17	AUGUSTUS	stop_codon	21441	21443	.	+	0	transcript_id "g1.t1"; gene_id "g1";
   85 chr17	AUGUSTUS	tts	21677	21677	.	+	.	transcript_id "g1.t1"; gene_id "g1";
   86 # protein sequence = [MPLHRYPVHLWQKLRLRQGICARLPAHFLRSLEEERTPTPVHYKPHGTKFKINPKNGQRERVEDVPIPVHYPPESQQG
   87 # LWGGEGLILGYRYANNDKLSKRVKKVWKPQLFTRELYSEILDKKFTVTVTMRTLDLIDEAYGFDFYILKTPKEDLGSKFGMDLKRGMLLRLARQDPHL
   88 # HPENPERRAAIYDKYRSFVIPEAEAEWVGLTLEEALEKQRLLEEKDPVPLFKVYVEELVQRLQEQVLSRPAVVQKRAGDHA]
   89 # Evidence for and against this transcript:
   90 # % of transcript supported by hints (any source): 100
   91 # CDS exons: 5/5
   92 #      W:   5 
   93 # CDS introns: 4/4
   94 #      E:   4 
   95 # 5'UTR exons and introns: 1/1
   96 #      W:   1 
   97 # 3'UTR exons and introns: 1/1
   98 #      W:   1 
   99 # hint groups fully obeyed: 68
  100 #      E:   4 
  101 #      W:  64 
  102 # incompatible hint groups: 41
  103 #      W:  41 
  104 # end gene g1
  105 ###