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Member "augustus-3.3.3/docs/tutorial-cgp/data/augCGP_rnaseq/pred8/monDom5.cgp.gff" (22 May 2019, 12931 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 'monDom5' -----
    9 #
   10 #----- prediction on sequence range chr6:167820-318655 (150836bp) -----
   11 #
   12 # start gene g1
   13 chr6	AUGUSTUS	gene	169620	178380	0	+	.	g1
   14 chr6	AUGUSTUS	transcript	169620	178380	.	+	.	g1.t1
   15 chr6	AUGUSTUS	CDS	169620	169752	0.94	+	2	transcript_id "g1.t1"; gene_id "g1";
   16 chr6	AUGUSTUS	exon	169620	169752	.	+	.	transcript_id "g1.t1"; gene_id "g1";
   17 chr6	AUGUSTUS	CDS	172808	172939	0.98	+	1	transcript_id "g1.t1"; gene_id "g1";
   18 chr6	AUGUSTUS	exon	172808	172939	.	+	.	transcript_id "g1.t1"; gene_id "g1";
   19 chr6	AUGUSTUS	CDS	173758	173833	0.99	+	1	transcript_id "g1.t1"; gene_id "g1";
   20 chr6	AUGUSTUS	exon	173758	173833	.	+	.	transcript_id "g1.t1"; gene_id "g1";
   21 chr6	AUGUSTUS	CDS	177296	177451	1	+	0	transcript_id "g1.t1"; gene_id "g1";
   22 chr6	AUGUSTUS	exon	177296	177451	.	+	.	transcript_id "g1.t1"; gene_id "g1";
   23 chr6	AUGUSTUS	CDS	177711	177813	0.98	+	0	transcript_id "g1.t1"; gene_id "g1";
   24 chr6	AUGUSTUS	exon	177711	177813	.	+	.	transcript_id "g1.t1"; gene_id "g1";
   25 chr6	AUGUSTUS	CDS	178169	178380	0.48	+	2	transcript_id "g1.t1"; gene_id "g1";
   26 chr6	AUGUSTUS	exon	178169	178380	.	+	.	transcript_id "g1.t1"; gene_id "g1";
   27 chr6	AUGUSTUS	stop_codon	178378	178380	.	+	0	transcript_id "g1.t1"; gene_id "g1";
   28 # protein sequence = [SSLYGYSLKELYEEITGKKSIFEEDPYLKKIINNVTHRMSPFHSSGAIRYLTNVPAKDILLVKSDACEMLDEQTLTTK
   29 # WTFNTSDVVRKPVFGYYKPDALAVVLENGTDDQRKIWIVDVASGALLWSLSLSLVPRSLKTATMQTADRRSVFFFWGSSNLTGPNQMETVNFQQILYL
   30 # FHPTLPDNLLEIANTTENIAAFNVLIFEESHHASYVLLTGPTNQDQPGQVTLSKQKVKENILNSKVIWLIKEKSDSDQIIKDRFYELRYRREK]
   31 # Evidence for and against this transcript:
   32 # % of transcript supported by hints (any source): 0
   33 # CDS exons: 0/6
   34 # CDS introns: 0/6
   35 # 5'UTR exons and introns: 0/0
   36 # 3'UTR exons and introns: 0/0
   37 # hint groups fully obeyed: 22
   38 #     RM:  22 
   39 # incompatible hint groups: 0
   40 # end gene g1
   41 ###
   42 # start gene g2
   43 chr6	AUGUSTUS	gene	187389	205172	0	-	.	g2
   44 chr6	AUGUSTUS	transcript	187389	205172	.	-	.	g2.t1
   45 chr6	AUGUSTUS	stop_codon	187389	187391	.	-	0	transcript_id "g2.t1"; gene_id "g2";
   46 chr6	AUGUSTUS	CDS	187389	187530	0.98	-	1	transcript_id "g2.t1"; gene_id "g2";
   47 chr6	AUGUSTUS	exon	187389	187530	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   48 chr6	AUGUSTUS	CDS	187884	187966	0.95	-	0	transcript_id "g2.t1"; gene_id "g2";
   49 chr6	AUGUSTUS	exon	187884	187966	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   50 chr6	AUGUSTUS	CDS	189106	189244	0.89	-	1	transcript_id "g2.t1"; gene_id "g2";
   51 chr6	AUGUSTUS	exon	189106	189244	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   52 chr6	AUGUSTUS	CDS	190181	190268	0.26	-	2	transcript_id "g2.t1"; gene_id "g2";
   53 chr6	AUGUSTUS	exon	190181	190268	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   54 chr6	AUGUSTUS	CDS	190930	191045	0.33	-	1	transcript_id "g2.t1"; gene_id "g2";
   55 chr6	AUGUSTUS	exon	190930	191045	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   56 chr6	AUGUSTUS	CDS	191435	191548	1	-	1	transcript_id "g2.t1"; gene_id "g2";
   57 chr6	AUGUSTUS	exon	191435	191548	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   58 chr6	AUGUSTUS	CDS	191911	191972	1	-	0	transcript_id "g2.t1"; gene_id "g2";
   59 chr6	AUGUSTUS	exon	191911	191972	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   60 chr6	AUGUSTUS	CDS	192243	192272	0.78	-	0	transcript_id "g2.t1"; gene_id "g2";
   61 chr6	AUGUSTUS	exon	192243	192272	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   62 chr6	AUGUSTUS	CDS	194272	194340	0.48	-	0	transcript_id "g2.t1"; gene_id "g2";
   63 chr6	AUGUSTUS	exon	194272	194340	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   64 chr6	AUGUSTUS	CDS	195381	195462	0.96	-	1	transcript_id "g2.t1"; gene_id "g2";
   65 chr6	AUGUSTUS	exon	195381	195462	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   66 chr6	AUGUSTUS	CDS	195994	196070	0.99	-	0	transcript_id "g2.t1"; gene_id "g2";
   67 chr6	AUGUSTUS	exon	195994	196070	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   68 chr6	AUGUSTUS	CDS	196285	196343	0.96	-	2	transcript_id "g2.t1"; gene_id "g2";
   69 chr6	AUGUSTUS	exon	196285	196343	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   70 chr6	AUGUSTUS	CDS	196838	196889	1	-	0	transcript_id "g2.t1"; gene_id "g2";
   71 chr6	AUGUSTUS	exon	196838	196889	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   72 chr6	AUGUSTUS	CDS	198977	199083	1	-	2	transcript_id "g2.t1"; gene_id "g2";
   73 chr6	AUGUSTUS	exon	198977	199083	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   74 chr6	AUGUSTUS	CDS	201139	201189	0.73	-	2	transcript_id "g2.t1"; gene_id "g2";
   75 chr6	AUGUSTUS	exon	201139	201189	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   76 chr6	AUGUSTUS	CDS	201939	202035	0.85	-	0	transcript_id "g2.t1"; gene_id "g2";
   77 chr6	AUGUSTUS	exon	201939	202035	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   78 chr6	AUGUSTUS	CDS	205110	205172	0.85	-	0	transcript_id "g2.t1"; gene_id "g2";
   79 chr6	AUGUSTUS	exon	205110	205172	.	-	.	transcript_id "g2.t1"; gene_id "g2";
   80 chr6	AUGUSTUS	start_codon	205170	205172	.	-	0	transcript_id "g2.t1"; gene_id "g2";
   81 # protein sequence = [MTINSLHQGGSYKVQMPCLSKMERVIVGMQDPDMGVKMRNQRLLITVIPHAMTGHDIVEWLIQKYSISEEESLHLGNL
   82 # IVKHGYIYPLKDPRCLVLRADDSPYRFQTPYFWMSTKWPAAELDYAIYLAKKNIRKQGDLIDHEKDYYNQLHKKINHTWDFVVMQAREQLRAAKQRRK
   83 # GDRIVIECQEQTYWLVNRPPPGALNVMEQGPERGNCYTSRVQMTKNMDFYKREIEYCKKAMSRTRVKSSICLEAYLKFNDQYMPHDPIMSGCLPSNPW
   84 # ITDDTDYWSMNAPTVPTPTKLRVERWAFNFRELLGDPLGHIQFMEFLKKEFSAENLSFWEACEDLRYGEQSKITESVDSVYQQFLAPGATRWVNIDSK
   85 # TMEKTLEGIRRPHRYVMDDAQMHIYMLMKKDSYPRFLKSDMYKTLLAEAVIPPETKKRVFPFMRKQRHSSPSPALFLPSGEQEPKGDDKGKALAPGTS
   86 # AGEGEV]
   87 # Evidence for and against this transcript:
   88 # % of transcript supported by hints (any source): 0
   89 # CDS exons: 0/17
   90 # CDS introns: 0/16
   91 # 5'UTR exons and introns: 0/0
   92 # 3'UTR exons and introns: 0/0
   93 # hint groups fully obeyed: 42
   94 #     RM:  42 
   95 # incompatible hint groups: 0
   96 # end gene g2
   97 ###
   98 # start gene g3
   99 chr6	AUGUSTUS	gene	220801	240996	0	+	.	g3
  100 chr6	AUGUSTUS	transcript	220801	240996	.	+	.	g3.t1
  101 chr6	AUGUSTUS	start_codon	220801	220803	.	+	0	transcript_id "g3.t1"; gene_id "g3";
  102 chr6	AUGUSTUS	CDS	220801	220873	0.72	+	0	transcript_id "g3.t1"; gene_id "g3";
  103 chr6	AUGUSTUS	exon	220801	220873	.	+	.	transcript_id "g3.t1"; gene_id "g3";
  104 chr6	AUGUSTUS	CDS	235116	235295	0.85	+	2	transcript_id "g3.t1"; gene_id "g3";
  105 chr6	AUGUSTUS	exon	235116	235295	.	+	.	transcript_id "g3.t1"; gene_id "g3";
  106 chr6	AUGUSTUS	CDS	239787	239870	0.93	+	2	transcript_id "g3.t1"; gene_id "g3";
  107 chr6	AUGUSTUS	exon	239787	239870	.	+	.	transcript_id "g3.t1"; gene_id "g3";
  108 chr6	AUGUSTUS	CDS	240133	240209	.	+	2	transcript_id "g3.t1"; gene_id "g3";
  109 chr6	AUGUSTUS	exon	240133	240209	.	+	.	transcript_id "g3.t1"; gene_id "g3";
  110 chr6	AUGUSTUS	CDS	240511	240574	0.51	+	0	transcript_id "g3.t1"; gene_id "g3";
  111 chr6	AUGUSTUS	exon	240511	240574	.	+	.	transcript_id "g3.t1"; gene_id "g3";
  112 chr6	AUGUSTUS	CDS	240797	240996	0.3	+	2	transcript_id "g3.t1"; gene_id "g3";
  113 chr6	AUGUSTUS	exon	240797	240996	.	+	.	transcript_id "g3.t1"; gene_id "g3";
  114 chr6	AUGUSTUS	stop_codon	240994	240996	.	+	0	transcript_id "g3.t1"; gene_id "g3";
  115 # protein sequence = [MLGLDMCELGAQVLELLWLTVCARDFMADKEGIRAVHEEDLDEVDLNYKAPEKKSLQEIQQLDQDDESLTKYKQALLG
  116 # SIPEAVDPSLPNVQVTRLTLVCEQAPGPITMDLTGDLESLKNQVFVLKEGVDYKVKISFKVNKEIVCGLKYLHVTYRKGLRVDKAMYMVGSYGPRTEE
  117 # YEFLTPMEEAPKGLLVRGTYRIKSFFTDDDKTDHLSWEWDLNIKKDWKD]
  118 # Evidence for and against this transcript:
  119 # % of transcript supported by hints (any source): 0
  120 # CDS exons: 0/6
  121 # CDS introns: 0/5
  122 # 5'UTR exons and introns: 0/0
  123 # 3'UTR exons and introns: 0/0
  124 # hint groups fully obeyed: 36
  125 #     RM:  36 
  126 # incompatible hint groups: 0
  127 # end gene g3
  128 ###
  129 # start gene g4
  130 chr6	AUGUSTUS	gene	242232	251839	0	+	.	g4
  131 chr6	AUGUSTUS	transcript	242232	251839	.	+	.	g4.t1
  132 chr6	AUGUSTUS	start_codon	242232	242234	.	+	0	transcript_id "g4.t1"; gene_id "g4";
  133 chr6	AUGUSTUS	CDS	242232	242445	0.3	+	0	transcript_id "g4.t1"; gene_id "g4";
  134 chr6	AUGUSTUS	exon	242232	242445	.	+	.	transcript_id "g4.t1"; gene_id "g4";
  135 chr6	AUGUSTUS	CDS	244205	244411	0.9	+	2	transcript_id "g4.t1"; gene_id "g4";
  136 chr6	AUGUSTUS	exon	244205	244411	.	+	.	transcript_id "g4.t1"; gene_id "g4";
  137 chr6	AUGUSTUS	CDS	246400	246533	0.25	+	2	transcript_id "g4.t1"; gene_id "g4";
  138 chr6	AUGUSTUS	exon	246400	246533	.	+	.	transcript_id "g4.t1"; gene_id "g4";
  139 chr6	AUGUSTUS	CDS	247263	247400	0.17	+	0	transcript_id "g4.t1"; gene_id "g4";
  140 chr6	AUGUSTUS	exon	247263	247400	.	+	.	transcript_id "g4.t1"; gene_id "g4";
  141 chr6	AUGUSTUS	CDS	247564	247680	.	+	0	transcript_id "g4.t1"; gene_id "g4";
  142 chr6	AUGUSTUS	exon	247564	247680	.	+	.	transcript_id "g4.t1"; gene_id "g4";
  143 chr6	AUGUSTUS	CDS	248241	248366	1	+	0	transcript_id "g4.t1"; gene_id "g4";
  144 chr6	AUGUSTUS	exon	248241	248366	.	+	.	transcript_id "g4.t1"; gene_id "g4";
  145 chr6	AUGUSTUS	CDS	248459	248656	1	+	0	transcript_id "g4.t1"; gene_id "g4";
  146 chr6	AUGUSTUS	exon	248459	248656	.	+	.	transcript_id "g4.t1"; gene_id "g4";
  147 chr6	AUGUSTUS	CDS	248995	249115	0.99	+	0	transcript_id "g4.t1"; gene_id "g4";
  148 chr6	AUGUSTUS	exon	248995	249115	.	+	.	transcript_id "g4.t1"; gene_id "g4";
  149 chr6	AUGUSTUS	CDS	249275	249456	1	+	2	transcript_id "g4.t1"; gene_id "g4";
  150 chr6	AUGUSTUS	exon	249275	249456	.	+	.	transcript_id "g4.t1"; gene_id "g4";
  151 chr6	AUGUSTUS	CDS	250098	250205	0.99	+	0	transcript_id "g4.t1"; gene_id "g4";
  152 chr6	AUGUSTUS	exon	250098	250205	.	+	.	transcript_id "g4.t1"; gene_id "g4";
  153 chr6	AUGUSTUS	CDS	251505	251549	0.99	+	0	transcript_id "g4.t1"; gene_id "g4";
  154 chr6	AUGUSTUS	exon	251505	251839	.	+	.	transcript_id "g4.t1"; gene_id "g4";
  155 chr6	AUGUSTUS	stop_codon	251547	251549	.	+	0	transcript_id "g4.t1"; gene_id "g4";
  156 chr6	AUGUSTUS	tts	251839	251839	.	+	.	transcript_id "g4.t1"; gene_id "g4";
  157 # protein sequence = [MRRYSLLFFVLTVWAWTLNGEGAGEEGVEAPEEATPEPPSDELLEEDDILVLTQHNFGRALQEHRYLLVEFYAPWCGH
  158 # CRALAPEYAKAASLLKNESSELKLAKVDGPAEKELAEEFGVTGYPALKFFKDGNRSQPVEFTGPREAEGIVRWLKRRLGPSATRLETEAEAAQFIDSQ
  159 # DIVIVGFFKDLQDEDVAGFLAIAEDAVDLTFGLTDRPELFQKYDLSRDTVVLFKKFDEGRADFPVDEELGLDQADLTHFLVVHSMHLVTEFNSQTSSK
  160 # IFEARILNHLLLFINQTLSPHRELLKGFQEAAPAFRGEILFVVVDVAGENDHVLQYFGMNATDAPTLRLINVETTKKYVPGAGGEITAASVSAFCQDV
  161 # LSGKVKPHLRSQEIPADWDQKPVKVLVGKNFEEVAFDASKNVFVKFYAPWCTHCKEMAQTWEDLAEKYKDREDIVIAELDSTANELEAFAIRGFPTLK
  162 # YFPAGPDRKVIEYKSSRDLETFSKFLDNGGVLPEPEPKEPEVPLPEAGANDSKDHKDEL]
  163 # Evidence for and against this transcript:
  164 # % of transcript supported by hints (any source): 0
  165 # CDS exons: 0/11
  166 # CDS introns: 0/10
  167 # 5'UTR exons and introns: 0/0
  168 # 3'UTR exons and introns: 0/1
  169 # hint groups fully obeyed: 19
  170 #     RM:  19 
  171 # incompatible hint groups: 0
  172 # end gene g4
  173 ###
  174 # start gene g5
  175 chr6	AUGUSTUS	gene	255158	300801	0	-	.	g5
  176 chr6	AUGUSTUS	transcript	255158	300801	.	-	.	g5.t1
  177 chr6	AUGUSTUS	tts	255158	255158	.	-	.	transcript_id "g5.t1"; gene_id "g5";
  178 chr6	AUGUSTUS	exon	255158	255616	.	-	.	transcript_id "g5.t1"; gene_id "g5";
  179 chr6	AUGUSTUS	stop_codon	255490	255492	.	-	0	transcript_id "g5.t1"; gene_id "g5";
  180 chr6	AUGUSTUS	CDS	255490	255616	0.95	-	1	transcript_id "g5.t1"; gene_id "g5";
  181 chr6	AUGUSTUS	CDS	259013	259180	1	-	1	transcript_id "g5.t1"; gene_id "g5";
  182 chr6	AUGUSTUS	exon	259013	259180	.	-	.	transcript_id "g5.t1"; gene_id "g5";
  183 chr6	AUGUSTUS	CDS	261886	261993	.	-	1	transcript_id "g5.t1"; gene_id "g5";
  184 chr6	AUGUSTUS	exon	261886	261993	.	-	.	transcript_id "g5.t1"; gene_id "g5";
  185 chr6	AUGUSTUS	CDS	267609	267854	0.82	-	1	transcript_id "g5.t1"; gene_id "g5";
  186 chr6	AUGUSTUS	exon	267609	267854	.	-	.	transcript_id "g5.t1"; gene_id "g5";
  187 chr6	AUGUSTUS	CDS	274074	274250	0.93	-	1	transcript_id "g5.t1"; gene_id "g5";
  188 chr6	AUGUSTUS	exon	274074	274250	.	-	.	transcript_id "g5.t1"; gene_id "g5";
  189 chr6	AUGUSTUS	CDS	276354	276901	1	-	0	transcript_id "g5.t1"; gene_id "g5";
  190 chr6	AUGUSTUS	exon	276354	276901	.	-	.	transcript_id "g5.t1"; gene_id "g5";
  191 chr6	AUGUSTUS	CDS	295021	295158	1	-	0	transcript_id "g5.t1"; gene_id "g5";
  192 chr6	AUGUSTUS	exon	295021	295158	.	-	.	transcript_id "g5.t1"; gene_id "g5";
  193 chr6	AUGUSTUS	CDS	300726	300801	0.3	-	1	transcript_id "g5.t1"; gene_id "g5";
  194 chr6	AUGUSTUS	exon	300726	300801	.	-	.	transcript_id "g5.t1"; gene_id "g5";
  195 # protein sequence = [DGVPPYRTRKQHRREMQESVKANGRRTYRMPKEIRVEPQKFAAELINRLEAVQRTREAEEKLEERLKRVRAEEEGEDA
  196 # NVSSGPPIVSHKLPSAQTLHHFPPRYTEMGCTGIRDVHEENPESILDEHVQRVMKTPGCQSPGPGHHSPKPRSPDNGHTAKIPGTLGTGPSGHSKHCT
  197 # KSGMKLDAANLYHHKHVYHHIHHHSVMKPKEQIEAEATQRVQNSFAWNAESHNYATKSRNYSENMGLTSNPVDGLGYSGKTSMLSKRNSKKADSGKSA
  198 # GSNYEMPGSPEDVEKNQKIMQWIIEGEKEISRHKKTNHGSSGTKKQLGHDSSRPLSIERPGAVHPWVSAQLRNVVQPSHLFIQDPTMPPNPAPNPLTQ
  199 # LEEARRRLEEEEKRTGKLPTKQRYVQEVIQRGRSSVRPACMPMLNVVPAVSDMDLSESEAKLQKKPGNSSAPPCDTIVVAYYFCGEPIPYRTLVKGRV
  200 # VTLGQFKELLTKKGNYRYYFKKVSDEFDCGVVFEEVREDDAILPIFEEKIIGKVEKVD]
  201 # Evidence for and against this transcript:
  202 # % of transcript supported by hints (any source): 0
  203 # CDS exons: 0/8
  204 # CDS introns: 0/8
  205 # 5'UTR exons and introns: 0/0
  206 # 3'UTR exons and introns: 0/1
  207 # hint groups fully obeyed: 60
  208 #     RM:  60 
  209 # incompatible hint groups: 0
  210 # end gene g5
  211 ###