GENSCAN 1.0 Date run: 2-Apr-107 Time: 21:38:30 Sequence Pan : 72050 bp : 47.45% 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 + 2641 3492 852 0 0 83 61 470 0.463 38.45 1.02 Term + 3671 3949 279 1 0 25 36 350 0.482 18.95 1.03 PlyA + 5735 5740 6 1.05 2.05 PlyA - 7493 7488 6 1.05 2.04 Term - 12518 12315 204 2 0 27 32 165 0.269 2.17 2.03 Intr - 20190 20032 159 0 0 48 81 60 0.630 1.48 2.02 Intr - 22083 22023 61 2 1 104 105 87 0.982 10.74 2.01 Init - 23576 23563 14 2 2 89 80 16 0.236 0.52 2.00 Prom - 24330 24291 40 -6.76 3.04 PlyA - 24347 24342 6 1.05 3.03 Term - 32303 32116 188 0 2 105 38 91 0.253 3.45 3.02 Intr - 36148 35936 213 2 0 54 110 80 0.248 5.49 3.01 Init - 36376 36352 25 1 1 71 90 16 0.258 -0.19 3.00 Prom - 38098 38059 40 -3.66 4.10 PlyA - 38218 38213 6 1.05 4.09 Term - 39159 38756 404 1 2 77 39 458 0.964 35.12 4.08 Intr - 39632 39598 35 1 2 103 78 33 0.947 1.67 4.07 Intr - 41266 41046 221 1 2 67 94 471 0.996 42.70 4.06 Intr - 42043 41918 126 1 0 50 75 202 0.999 15.98 4.05 Intr - 42305 42141 165 2 0 80 81 287 0.918 27.36 4.04 Intr - 42926 42831 96 2 0 87 15 176 0.979 10.41 4.03 Intr - 43690 43630 61 0 1 117 100 78 0.996 10.64 4.02 Intr - 45652 45438 215 1 2 104 53 254 0.999 21.01 4.01 Init - 47341 46742 600 1 0 63 100 587 0.637 52.69 4.00 Prom - 49930 49891 40 -7.76 5.10 PlyA - 58973 58968 6 1.05 5.09 Term - 60171 59852 320 1 2 112 43 347 0.911 27.64 5.08 Intr - 60685 60651 35 0 2 109 84 15 0.993 1.07 5.07 Intr - 61239 61019 221 0 2 102 99 569 0.999 56.50 5.06 Intr - 61629 61504 126 0 0 74 75 157 0.999 13.88 5.05 Intr - 62216 62052 165 2 0 64 98 273 0.979 26.06 5.04 Intr - 62619 62524 96 0 0 91 40 184 0.631 14.11 5.03 Intr - 63036 62976 61 2 1 83 116 80 0.999 9.04 5.02 Intr - 64147 63927 221 1 2 82 81 383 0.999 34.10 5.01 Init - 65858 65214 645 2 0 88 90 751 0.584 70.62 5.00 Prom - 65972 65933 40 -0.86Click here to view a PDF image of the predicted gene(s)
Click here for a PostScript image of the predicted gene(s)
Predicted peptide sequence(s):
>Pan|GENSCAN_predicted_peptide_1|376_aa
MMHHLPRRKGSDHGLLTESKIETRTGSLPHLKIGSSIIQGTDIEEAAILAFVLVPNLQKK
NDGTKNKNEIRTGIGIRRTNIKTMMGTDGTRTRNDPVSPGRVKDFKSRKDGDSKKDEEDE
HGDRKRQAQLFSLEELLAKKKAKEEAEVKPKFLSKAEQEAEALKQWQQEVEEQQRMLVEE
RKKGNSSKTWAGRCWKILSNGNVGNTGRGWSQRPVEMRMRKGSRGYGKRRIRAKNCMPLS
EHTLGGIKKRHQTRHLNDRKLVFEGDASEDTSIDYNPLYKERHQKKLDEMTDRDWWLFRE
GYSITTKGGKIPNPIRSWKESSLPPHILEVIDKSGYKESTPNQHQAIPFGLQNRDIIGVA
ETGSSKTAAFLIPLLV
>Pan|GENSCAN_predicted_peptide_2|145_aa
MVDHRYEDEFHKYSEADNDFMVLKKGTSTLQHWILCIRIEATIARRQMDRENIQLIHLWS
WVHDYQLVLGNVCHSCCKGLACNGHLRRQTVTEQSILIAAVVNRTSSSKNISMGDSSSSS
SGDWSNRGTQGLQGGINSTAIGKDV
>Pan|GENSCAN_predicted_peptide_3|141_aa
MVEGATKEVALNHVPVEHMVKLQGEGIKSEARIGAGENRTFLRLWETGNLGLSQPCRIPQ
PIAHLKAELGQLFAFEGSQGALVLSSPPSSGEPDPCTTIPPGKSPRSQSYIYPSPILWFH
IGKKLLLLSSCLPEARTPTAP
>Pan|GENSCAN_predicted_peptide_4|640_aa
MNRQVCKKSFSGRSQGFSGRSAVVSGSSRMSCVAHSGGAGGGACGFRSGAGSFGSRSLYN
LGSNKSISISVAAGGSRAGGFGGGRSSCGFAGGYGGGFGGSYGGGFGGGRGVGSGFGGAG
GFGGAGGFGGPGVFGGPGSFGGPGGFGPGGFPGGIQEVIVNQSLLQPLNVEIDPQIGQVK
AQEREQIKTLNNKFASFIDKVRFLEQQNKVLETKWELLQQQTTGSGPSSLEPCFESYISF
LRKQLDSLLGERGNLEGELKSMQDLVEDFKKKYEDEINKRTAAENEFVGLKKDVDAAFMS
KVELQAKVDSLTDEVSFLRTLYEMELSQMQSHASDTSVVLSMDNNRCLDLDSIIAEVRAQ
YEEIAQRSKAEAEALYQTKLGELQTTAGRHGDDLRNTKSEIMELNRMIQRLRAEIENVKK
QNANLQTAIAEAEQRGEMALKDANAKLQDLQAALQKAKDDLARLLRDYQELMNVKLALDV
EIATYRKLLEGEECRMSGECQSAVCISVVSNVTSTSGSSGSSRAVFGGVSGSGSGGYKGG
SSSSSSSSSGYGVSGGSGSGYGGVSSGSTGGRGSSGSYQSSSSGSRLGGAGGISVSHSGM
DSSSGSIQTSGGSGYKSGGGGSTSIRFSQTTSSSQHSSTK
>Pan|GENSCAN_predicted_peptide_5|629_aa
MSRQASKTSGGGSQGFSGRSAVVSGSSRMSCAARSGGAGGGAYGFRSGAGGFGSRSLYNL
GGNKSISISVAAGGSRAGGFGGGRSSCGFAGGYGGGFGGGYGGGFGGGFGGGRGMGGGFG
GAGGFGGAGGFGGAGGFGGPGGFGGPGVFGGPGSFGSPGGFGPGGFPGGIQEVTINQSLL
QPLNVEIDPQIGQVKAQEREQIKTLNNKFASFIDKVRFLEQQNKVLETKWNLLQQQGTSS
ISGTNNLEPLFENHINYLRSYLDNILGERGRLDSELKNMEDLVEDFKKKYEDEINKRTAA
ENEFVTLKKDVDSAYMNKVELQAKVDALIDEIDFLRTLYDAELSQMQSHISDTSVVLSMD
NNRSLDLDSIIAEVRAQYEDIAQRSKAEAEALYQTKLGELQTTAGRHGDDLRNTKSEIIE
LNRMIQRLRAEIEGVKKQNANLQTAIAEAEQHGEMALKDANAKLQELQAALQQAKDDLAR
LLRDYQELMNVKLALDVEIATYRKLLEGEEYRMSGECPSAVSISVVSSSTTSASAGGYGG
GYGGGLGGGLGGGFSAGGGSGSGFGRGGGGGIGGGFGGGSSSGFSGGSGFGSISGARYGV
SGGGFSSASNRGGSIKFSQSSQSSQRYSR
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.