GENSCAN 1.0 Date run: 19-Mar-108 Time: 07:39:54 Sequence poulet2 : 10686 bp : 43.79% C+G : Isochore 2 (43 - 51 C+G%) Parameter matrix: HumanIso.smat Predicted genes/exons: Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr.. ----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------ 1.01 Init + 291 619 329 2 2 82 13 167 0.343 3.40 1.02 Intr + 684 759 76 0 1 113 103 130 0.997 16.52 1.03 Intr + 1166 1345 180 1 0 136 36 187 0.849 18.36 1.04 Intr + 1472 1537 66 1 0 65 115 38 0.897 3.30 1.05 Intr + 2711 2829 119 1 2 68 119 63 0.995 6.66 1.06 Intr + 3556 3625 70 1 1 113 34 39 0.569 0.18 1.07 Intr + 3982 4116 135 0 0 90 60 186 0.999 16.76 1.08 Intr + 4561 4750 190 0 1 111 67 161 0.999 15.46 1.09 Intr + 6600 6730 131 1 2 66 113 141 0.999 14.81 1.10 Intr + 6873 7006 134 2 2 89 86 129 0.998 12.24 1.11 Intr + 7308 7407 100 0 1 88 109 123 0.999 14.51 1.12 Intr + 8781 8903 123 2 0 115 96 3 0.520 4.58Click here to view a PDF image of the predicted gene(s)
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Predicted peptide sequence(s): >poulet2|GENSCAN_predicted_peptide_1|551_aa MRCPPQGAAPPSGAGAAFRRAFEAAPAALPASPPRRQERGSPRVERDSSGRGEEGGKGAA AAGSRALGQPDDGPRPLPGFAPRAEPGPGAEAEWRLVGRRPPVPEGGTSEADIALIGLAV MGQNLILNMNDHGFVVCAFNRTVSKVDDFLANEAKGTKVIGAHSLEEMVSKLKKPRRIIL LVKAGSAVDDFINKLVPLLETGDIIIDGGNSEYRDTTRRCKELLQKGLLFVGSGVSGGEE GARYGPSLMPGGSKEAWPHIKTIFQSIAAKVGSGEPCCDWVGEEGAGHFVKMVHNGIEYG DMQLICEAYHLMKDVVGMDHDEMSQVFEEWNNTELDSFLIEITANILKFKDKDGKYLLPK IRDSAGQKGTGKWTAISALEYGVPVTLIGEAVFARCLSSLKDERVQASKLLNGPKLTQFS GNKKAFLEDIRKALYASKIISYAQGFMLLRQAAKEFGWTLNYGGIALMWRGGCIIRSVFL GKIKDAFDRNPELQNLLLDDFFKTAVEKCQDSWRHVISTGVQHGIPMPCFTTALSFYDGY RHEVLPANLIQ Explanation 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 (sum over all parses containing exon) Tscr : exon score (depends on length, I/Ac, Do/T and CodRg scores) 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 GENSCAN'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.