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GenomeScan 1.0 Date run: 24-Nov-2003 Time: 12:01:25 Sequence HS307871 : 4514 bp : 52.19% C+G : Isochore 3 (51 - 57 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 Intr + 739 851 113 0 2 49 66 74 0.000 0.98 1.02 Intr + 1748 1860 113 2 2 53 110 80 0.000 24.16 1.03 Intr + 1976 2055 80 0 2 97 94 10 0.000 19.07 1.04 Intr + 2132 2194 63 1 0 84 80 87 0.000 26.53 1.05 Intr + 2434 2631 198 0 0 88 -9 263 0.000 33.51 1.06 Intr + 2749 2910 162 0 0 107 109 97 0.000 28.74 1.07 Intr + 3279 3416 138 2 0 52 77 126 0.000 27.22 1.08 Intr + 3576 3676 101 2 2 87 119 113 0.000 33.81 1.09 Intr + 3780 3846 67 0 1 63 77 46 0.000 15.73 1.10 Term + 4179 4340 162 2 0 75 47 276 0.000 57.52 1.11 PlyA + 4397 4402 6 1.05 Genoa hits used in predictions: 17 nonredundant hits explanation Genoa hit name Target protein P.beg P.end G.beg G.end RF Program E-val -------------- -------------- ----- ----- ----- ----- -- ------- ----- Hit1.1_Hit3.1.i gi|2507533|sp|P06132|DCUP_HUMAN+ 158 162 2661 2728 0 BLASTX 1e-31 Hit3.1_Hit4.1.i gi|2507533|sp|P06132|DCUP_HUMAN+ 212 213 2940 3249 2 BLASTX 1e-28 Hit9.1_Hit1.1.i gi|2507533|sp|P06132|DCUP_HUMAN+ 92 92 2224 2401 0 BLASTX 9.65e-17 Hit5.1_Hit7.1.i gi|2507533|sp|P06132|DCUP_HUMAN+ 44 45 1889 1945 0 BLASTX 1.93e-16 Hit7.1_Hit9.1.i gi|2507533|sp|P06132|DCUP_HUMAN+ 71 70 2085 2096 1 BLASTX 1.93e-16 Hit4.1_Hit6.1.i gi|2507533|sp|P06132|DCUP_HUMAN+ 259 259 3449 3546 2 BLASTX 3e-16 Hit8.1_Hit2.1.i gi|2507533|sp|P06132|DCUP_HUMAN+ 314 309 3876 4131 2 BLASTX 3e-16 Hit6.1_Hit8.1.i gi|2507533|sp|P06132|DCUP_HUMAN+ 292 291 3707 3745 0 BLASTX 6e-16 Hit1.1 gi|2507533|sp|P06132|DCUP_HUMAN+ 92 158 2431 2631 0 BLASTX 1e-42 Hit2.1 gi|2507533|sp|P06132|DCUP_HUMAN+ 309 367 4161 4337 2 BLASTX 1e-36 Hit3.1 gi|2507533|sp|P06132|DCUP_HUMAN+ 162 212 2758 2910 0 BLASTX 1e-31 Hit4.1 gi|2507533|sp|P06132|DCUP_HUMAN+ 213 259 3279 3419 2 BLASTX 1e-28 Hit5.1 gi|2507533|sp|P06132|DCUP_HUMAN+ 8 44 1749 1859 2 BLASTX 9.65e-17 Hit7.1 gi|2507533|sp|P06132|DCUP_HUMAN+ 45 71 1975 2055 0 BLASTX 9.65e-17 Hit9.1 gi|2507533|sp|P06132|DCUP_HUMAN+ 70 92 2126 2194 1 BLASTX 9.65e-17 Hit6.1 gi|2507533|sp|P06132|DCUP_HUMAN+ 259 292 3576 3677 2 BLASTX 3e-16 Hit8.1 gi|2507533|sp|P06132|DCUP_HUMAN+ 291 314 3775 3846 0 BLASTX 3e-16 Predicted peptide sequence(s): >HS307871|GenomeScan_predicted_peptide_1|398_aa:gi|2507533|sp|P06132|DCUP_HUMAN+:92..158:E=1e-42 VQAIVWTWLDKTVGIIVGTCAKLRIPRLSDENKFLMSPPQGFPELKNDTFLRAAWGEETD YTPVWCMRQAGRYLPEFRETRAAQDFFSTCRSPEACCELTLQPLRRFLLDAAIIFSDILV VPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQRLAGRV PLIGFAGAPWTLMTYMVEGGGSSTMAQAKRWLYQRPQASHQLLRILTDALVPYLVGQVVA GAQALQLFESHAGHLGPQLFNKFALPYIRDVAKQVKARLREAGLAPVPMIIFAKDGHFAL EELAQAGYEVVGLDWTVAPKKARECVGKTVTLQGNLDPCALYASEEEIGQLVKQMLDDFG PHRYIANLGHGLYPDMDPEHVGAFVDAVHKHSRLLRQN 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.