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GenomeScan 1.0 Date run: 26-Mar-2003 Time: 12:44:25 Sequence AC091491 : 152882 bp : 38.35% C+G : Isochore 1 ( 0 - 43 C+G%) Options: GenoaOnly BothStrands Parameter matrix: HumanIso.smat Predicted genes/exons: explanation Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr.. ----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------ 1.01 PlyA + 8915 8920 6 1.05 2.11 PlyA - 9099 9094 6 1.05 2.10 Term - 9458 9279 180 2 0 85 55 213 0.000 14.33 2.09 Intr - 19259 19056 204 2 0 31 67 103 0.000 0.97 2.08 Intr - 31235 31126 110 0 2 91 65 52 0.000 2.28 2.07 Intr - 34701 34598 104 2 2 49 100 17 0.000 -2.10 2.06 Intr - 53767 53686 82 2 1 68 102 50 0.000 2.18 2.05 Intr - 56317 56242 76 1 1 106 111 67 0.000 8.97 2.04 Intr - 61689 61582 108 0 0 79 31 89 0.000 1.86 2.03 Intr - 84483 84280 204 0 0 69 101 212 0.000 19.07 2.02 Intr - 89517 87031 2487 0 0 111 96 1876 0.000 554.57 2.01 Init - 104263 104213 51 1 0 34 93 49 0.000 1.21 2.00 Prom - 111210 111171 40 -3.65 Genoa hits used in predictions: 25 nonredundant hits explanation Genoa hit name Target protein P.beg P.end G.beg G.end RF Program E-val -------------- -------------- ----- ----- ----- ----- -- ------- ----- Hit2.10L gi|23396799|sp|Q8R3B1|PID1_MOUSE+ 730 754 87285 87205 3 BLASTX 9.99e-11 Hit2.9 gi|23396799|sp|Q8R3B1|PID1_MOUSE+ 704 730 87363 87286 3 BLASTX 9.99e-11 Hit3.15L gi|130228|sp|P10688|PID1_RAT+ 412 429 88248 88168 3 BLASTX 2.15e-07 Hit3.14 gi|130228|sp|P10688|PID1_RAT+ 386 412 88326 88249 3 BLASTX 2.15e-07 Hit3.13 gi|130228|sp|P10688|PID1_RAT+ 360 386 88404 88327 3 BLASTX 2.15e-07 Hit3.12 gi|130228|sp|P10688|PID1_RAT+ 334 360 88482 88405 3 BLASTX 2.15e-07 Hit3.11 gi|130228|sp|P10688|PID1_RAT+ 308 334 88560 88483 3 BLASTX 2.15e-07 Hit2.8 gi|23396799|sp|Q8R3B1|PID1_MOUSE+ 678 704 87441 87364 3 BLASTX 9.99e-11 Hit2.7 gi|23396799|sp|Q8R3B1|PID1_MOUSE+ 652 678 87519 87442 3 BLASTX 9.99e-11 Hit2.6 gi|23396799|sp|Q8R3B1|PID1_MOUSE+ 626 652 87597 87520 3 BLASTX 9.99e-11 Hit2.5 gi|23396799|sp|Q8R3B1|PID1_MOUSE+ 600 626 87675 87598 3 BLASTX 9.99e-11 Hit2.4 gi|23396799|sp|Q8R3B1|PID1_MOUSE+ 574 600 87753 87676 3 BLASTX 9.99e-11 Hit2.3 gi|23396799|sp|Q8R3B1|PID1_MOUSE+ 548 574 87831 87754 3 BLASTX 9.99e-11 Hit2.2 gi|23396799|sp|Q8R3B1|PID1_MOUSE+ 522 548 87909 87832 3 BLASTX 9.99e-11 Hit2.1 gi|23396799|sp|Q8R3B1|PID1_MOUSE+ 496 522 87987 87910 3 BLASTX 9.99e-11 Hit3.10 gi|130228|sp|P10688|PID1_RAT+ 282 308 88638 88561 3 BLASTX 2.15e-07 Hit3.9 gi|130228|sp|P10688|PID1_RAT+ 256 282 88716 88639 3 BLASTX 2.15e-07 Hit3.8 gi|130228|sp|P10688|PID1_RAT+ 230 256 88794 88717 3 BLASTX 2.15e-07 Hit3.7 gi|130228|sp|P10688|PID1_RAT+ 204 230 88872 88795 3 BLASTX 2.15e-07 Hit3.6 gi|130228|sp|P10688|PID1_RAT+ 178 204 88950 88873 3 BLASTX 2.15e-07 Hit3.5 gi|130228|sp|P10688|PID1_RAT+ 152 178 89028 88951 3 BLASTX 2.15e-07 Hit3.4 gi|130228|sp|P10688|PID1_RAT+ 126 152 89106 89029 3 BLASTX 2.15e-07 Hit3.3 gi|130228|sp|P10688|PID1_RAT+ 100 126 89184 89107 3 BLASTX 2.15e-07 Hit3.2 gi|130228|sp|P10688|PID1_RAT+ 74 100 89262 89185 3 BLASTX 2.15e-07 Hit3.1 gi|130228|sp|P10688|PID1_RAT+ 48 74 89340 89263 3 BLASTX 2.15e-07 Predicted peptide sequence(s): >AC091491|GenomeScan_predicted_peptide_2|1201_aa:gi|23396799|sp|Q8R3B1|PID1_MOUSE+:730..754:E=1e-100 MEEARAEIGESELECPKDGTKQKRERKKTVSFSSMPTEKKISSASDCINSMVEGSELKKV RSNSRIYHRYFLLDADMQSLRWEPSKKDSEKAKIDIKSIKEVRTGKNTDIFRSNGISDQI SEDCAFSVIYGENYESLDLVANSADVANIWVTGLRYLISYGKHTLDMLESSQDNMRTSWV SQMFSEIDVDNLGHITLCNAVQCIRNLNPGLKTSKIELKFKELHKSKDKAGTEVTKEEFI EVFHELCTRPEIYFLLVQFSSNKEFLDTKDLMMFLEAEQGVAHINEEISLEIIHKYEPSK EGQEKGWLSIDGFTNYLMSPDCYIFDPEHKKVCQDMKQPLSHYFINSSHNTYLIEDQFRG PSDITGYIRALKMGCRSVELDVWDGPDNEPVIYTGHTMTSQIVFRSVIDIINKYAFFASE YPLILCLENHCSIKQQKVMVQHMKKLLGDKLYTTSPNVEESYLPSPDVLKGKILIKAKKL SSNCSGVEGDVTDEDEGAEMSQRMGKENMEQPNNVPVKRFQLCKELSELVSICKSVQFKE FQVSFQVQKYWEVCSFNEVLASKYANENPGDFVNYNKRFLARVFPSPMRIDSSNMNPQDF WKCGCQIVAMNFQTPGLMMDLNIGWFRQNGNCGYVLRPAIMREEVSFFSANTKDSVPGVS PQLLHIKIISGQNFPKPKGSGAKGDVVDPYVYVEIHGIPADCAEQRTKTVHQNGDAPIFD ESFEFQINLPELAMVRFVVLDDDYIGDEFIGQYTIPFECLQTGYRHVPLQSLTGEVLAHA SLFVHVAITNRRGGGKPHKRGLSVRKGKKSREYASLRTLWIKTVDEVFKNAQPPIRDATD LRENMQNAVVSFKELCGLSSVANLMQCMLAVSPRFLGPDNTPLVVLNLSEQYPTMELQGI VPEVLKKIVTTYDMQLKDFSDFVTSLETATTEDAVATSVLSRTGKESSLEMIQSLKALIE NADAVYEKIVHCQKAGTCYADVSTGKRKRGRRGMLRSEDLQPSVCEVPGKLPCDSLGCVS FVLALALACHRETVKSQAMEFHEHLHSIGTKEGLKERKLQKAVESFTWNITILKKHLFGS SKNQGQELCLEGSPFRSCTEPFIPLWQLLCTLWGGGQGGGKAVFLLWGDKLICSSCSMPI KRGQADLLKYAKNETLENLKQIHFAAVSCGLNKPGTENADVQKPRRSLEVIPEKANDETG E Explanation Predicted genes/exons Gn.Ex : gene number, exon number (for reference) Type : Init = Initial exon (ATG to 5' splice site) Intr = Internal exon (3' splice site to 5' splice site) Term = Terminal exon (3' splice site to stop codon) Sngl = Single-exon gene (ATG to stop) Prom = Promoter (TATA box / initation site) PlyA = poly-A signal (consensus: AATAAA) S : DNA strand (+ = input strand; - = opposite strand) Begin : beginning of exon or signal (numbered on input strand) End : end point of exon or signal (numbered on input strand) Len : length of exon or signal (bp) Fr : reading frame (a forward strand codon ending at x has frame x mod 3) Ph : net phase of exon (exon length modulo 3) I/Ac : initiation signal or 3' splice site score (tenth bit units) Do/T : 5' splice site or termination signal score (tenth bit units) CodRg : coding region score (tenth bit units) P : probability of exon (not calculated for GenomeScan) Tscr : exon score (depends on length, I/Ac, Do/T and CodRg scores) Genoa hits used Genoa hit name: names ending in ".i" are predicted introns Target Protein: protein in which the hit is located P.beg : position of beginning in protein P.end : position of end in protein G.beg : position of beginning in DNA (nucleotide position on forward strand) G.end : position of end in DNA (nucleotide position on forward strand) RF : reading frame (forward strand codon ending at x has frame x mod 3) Program : name of program used for alignments, for reference E-val : probability that this is not a correct prediction Comments The SCORE of a predicted feature (e.g., exon or splice site) is a log-odds measure of the quality of the feature based on local sequence properties. For example, a predicted 5' splice site with score > 100 is strong; 50-100 is moderate; 0-50 is weak; and below 0 is poor (more than likely not a real donor site). The PROBABILITY of a predicted exon is the estimated probability under GenomeScan's model of genomic sequence structure that the exon is correct. This probability depends in general on global as well as local sequence properties, e.g., it depends on how well the exon fits with neighboring exons. It has been shown that predicted exons with higher probabilities are more likely to be correct than those with lower probabilities.