GENSCANW output for sequence 13:55:22
GENSCAN 1.0 Date run: 10-Apr-107 Time: 13:55:39
Sequence NW_876258.1 : 110002 bp : 36.25% C+G : Isochore 1 ( 0 - 43 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..
----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------
1.06 PlyA - 243 238 6 1.05
1.05 Term - 7184 6555 630 2 0 100 34 343 0.970 23.43
1.04 Intr - 24007 23893 115 0 1 48 69 124 0.023 6.03
1.03 Intr - 39455 39308 148 0 1 81 4 48 0.005 -5.93
1.02 Intr - 42376 42235 142 1 1 47 36 136 0.044 3.31
1.01 Init - 56996 56247 750 2 0 82 100 302 0.694 25.55
1.00 Prom - 57225 57186 40 -8.65
2.09 PlyA - 57240 57235 6 -4.04
2.08 Term - 58535 57435 1101 2 0 -10 42 463 0.162 22.98
2.07 Intr - 59334 59093 242 1 2 30 99 186 0.195 10.25
2.06 Intr - 64714 64590 125 0 2 69 36 74 0.033 -0.39
2.05 Intr - 81302 81161 142 0 1 90 95 136 0.382 12.99
2.04 Intr - 96784 96581 204 2 0 42 92 296 0.929 23.65
2.03 Intr - 97618 97219 400 1 1 71 51 514 0.947 39.15
2.02 Intr - 97943 97802 142 1 1 63 64 128 0.298 7.33
2.01 Init - 100307 100279 29 2 2 45 68 25 0.214 -4.68
2.00 Prom - 101408 101369 40 -5.85
3.00 Prom + 102421 102460 40 -9.25
3.01 Init + 102891 103254 364 2 1 78 71 261 0.894 20.66
3.02 Intr + 103385 103636 252 0 0 -77 68 370 0.544 14.98
3.03 Term + 103651 104177 527 2 2 -7 51 669 0.598 47.14
3.04 PlyA + 104215 104220 6 1.05
Predicted peptide sequence(s):
Predicted coding sequence(s):
>NW_876258.1|GENSCAN_predicted_peptide_1|594_aa
MNYWDFIKIRSFCTAKDTVNKTQRQPTEWEKIFANDISDKGLLSKIYKELLKLNTKETNN
PIKKWAKDMKRNLTEEDIDMANMHMRKCSASLAIREIQIKTTMRYHLTPGRMGKINKAGN
HKCWRGCGEKGTLLQCWWECEVVQPLWKTVWRFLKELKIYLPYDPAIALLGIYPKDTDAM
KRRDTCTPIFIAAMATIAKLWKEPRCPSKDEWIKKMWFMYTMEYYSAIRNDKYPPFASTW
MELEGIMLSEILFMRDRERMTERKKEAETQAEGEAGSMQGARHRTRSRVSRIRPWAEELF
IHETQRGRDRQKEKQAPFREPDAGLNPRTPGSQLEPKANIQPLYHPWLLQTSGKIRLLDV
GSCFNPFLKFEEFLTVGIDIVPAVESVYKCDFLNLQLQQPLQLAQDAIDAFLKQLKNPID
SLPGELFHVVVFSLLLSYFPSPYQRWICCKKAHELLVLNGLLLIITPDSSHQNRHAMMMK
SWKIAIESLGFKRFKYSKFSHMHLMAFRKTSLKTTSDLVSRNYPGMLYIPQDFNSIEEEE
YSNPSCYVRSDIEDEQLAYGFTELPDAPYDSDSGESQASSIPFYELEDPILLLS
>NW_876258.1|GENSCAN_predicted_CDS_1|1785_bp
atgaactattgggacttcattaagataagaagcttttgcacagcaaaggatacagtcaac
aaaactcaaagacaacctacagaatgggagaagatatttgcaaatgacatatcagataaa
gggctactttccaagatctataaagaacttcttaaactcaacaccaaagaaacaaacaat
ccaatcaagaaatgggcaaaagacatgaagagaaatctcacagaggaagacatagacatg
gccaacatgcacatgagaaaatgctctgcatcacttgccatcagggaaatacaaatcaaa
accacaatgagataccacctcacaccagggagaatggggaaaattaacaaggcaggaaac
cacaaatgttggagaggatgtggagaaaagggaaccctcttacagtgttggtgggaatgt
gaagtggtgcagccactctggaaaactgtgtggaggttcctcaaagagttaaaaatatac
ctgccctacgacccagcaattgcactgttggggatttatcccaaagatacagatgcaatg
aaacgcagggacacctgcaccccgatatttatagcagcaatggccacaatagccaagctg
tggaaggagcctcggtgtccatcaaaagatgagtggataaaaaagatgtggtttatgtat
acaatggaatattactcagccattagaaatgacaaatacccaccatttgcttcaacatgg
atggaactggagggtattatgctgagtgaaattttattcatgagagacagagagagaatg
acggaaagaaagaaagaggcagaaacacaggcagagggagaagcaggctccatgcaggga
gcccgacacaggactcgatcccgggtctccaggatcaggccctgggctgaagagttattt
attcacgagacacagagaggcagagataggcagaaggagaagcaggctccctttagggag
cctgatgcaggactcaatcccaggactccaggatcacaacttgagccaaaggcaaacatt
caaccactgtaccacccatggttgctacagacctcaggaaagatcagattacttgatgtt
ggcagctgctttaacccatttctgaagtttgaagaatttctaactgttggcatagacatc
gtacctgctgtagagagtgtatataaatgtgacttcctgaacttgcagcttcagcagcca
ctccagcttgcgcaggatgctatagatgcctttttgaagcagctgaaaaaccctatcgat
tctcttcctggagaacttttccatgtggtggttttctctctcctcctttcttattttcca
tcgccttaccaacggtggatttgctgcaagaaagcccatgaactgttagtgttaaatggt
ttattgcttatcatcacacctgattcctcccatcagaaccgtcatgctatgatgatgaaa
agctggaagattgctatagaatccctgggctttaaacgtttcaagtattcaaaattttca
catatgcatttgatggcatttagaaaaacctccctaaaaaccacaagtgacttggttagt
aggaactacccagggatgttatatattcctcaagatttcaacagtatagaagaggaggaa
tattctaatccttcgtgctacgttcgatcagatatagaagatgaacaactagcatatggt
ttcacagagctccctgatgctccatacgactcagattctggagaaagtcaagccagctct
attcctttctatgagctagaagatcctatattacttttaagttaa
>NW_876258.1|GENSCAN_predicted_peptide_2|794_aa
MNITANKEDRSSRPRAAASVPTAGANTARARISGEQGRNQQPHSPAISKEEGEEGPQTLR
RHLLPWPSAFPTSWVLCAALALQALPARASRASRAARASRAARAARARSPRSAGRPLLGA
NESISARVPRSVKLPSVLSTPLQSAPPRCAAAENLYVTKFGGARGAGSEPLRARTLMSLR
TARPGDARRAGVCGGPRGGGGGGGDMEPEAGGRGGARRPGAGPPSTPPPREQERKLEQEK
LSGVVKSVHRRLRKKYREVGDFDKIWREHCEDEETLCEYAVAMKNLADNHWAKTCEGEGR
IEWCCSVCREYFQNGGKRKALEKDEKRAVLATKTTPALNSHESSKLEDHNALKLELNHNK
KFGRTSNTWRLRTILLKDERVNQEIKEELKRFMETNENEDKTVQNLWDVAKAVLRGKYIT
IQASIQKLLFGKIERDGVLPNSFYEASITLIPKPDKDPTKKENYRPISLMNMDVKILNKI
LANRIQQHIKKIIHHDQVGFIPGTQGWFNTRKTISVIHHISKRKTKNHMILSLDAEKAFD
KIQHPFLIKTLQSVGIEGTFLDILKAIYEKPTANIILNGEALGTFPLRSGTRQGCPLSPL
LFNIVLEVLASAIRQQKDIKGIQIGKEEVKLSLFADDMILYIENPKVSTPRLLELIQQFG
SVAGYKINAQKSVAFLYTNNETEEREIKESIPFTIAPKSIRYLGINLTKDVKDLYPQNYR
TLLKEIEEDTKRWKNIPCSGIGRINIVKMSMLPRAIYTFNAIPIKIPWTFFRELEQIILR
FVWNQKRPRIAREF
>NW_876258.1|GENSCAN_predicted_CDS_2|2385_bp
atgaatataactgcaaacaaagaagacaggagctctcggcctcgggcagccgcctcggta
ccaaccgcaggagctaatacggcccgcgcacgcatctccggggagcaagggcgcaatcag
cagccacactccccagcaatttccaaagaggagggcgaggaggggccgcagaccctccgc
cgtcacctccttccgtggccctcggctttccccacttcctgggtcctctgcgcagctctg
gcgctgcaggcactgccggcccgtgcatcccgtgcatcccgagcagcccgtgcatcccgt
gcagcccgagcagcccgtgcacgaagtccacgctccgcaggccgacctctcctgggcgcc
aacgagagcatctccgctcgggtccctcggagcgtaaaactcccgtcggtgctgtcgact
ccgctccaaagcgctcccccgcgctgcgcagccgcagagaacctctacgtgacaaagttc
ggcggcgctcggggcgcaggctccgagccgctccgcgctaggacgctgatgtctctgcgg
accgcacggccgggagacgccaggcgggcgggcgtctgcgggggcccgaggggcggcggc
ggcggcggcggcgacatggagccggaggccggcggccgaggcggtgctcgcaggcctggg
gctgggcccccgagcaccccgccgcctcgggagcaggagcggaagctggagcaggagaag
ctctccggggtggtgaagagcgtccaccggcggctccgcaagaagtaccgggaagtggga
gattttgataagatctggcgagaacattgtgaggatgaggaaacactttgtgaatacgct
gttgcaatgaaaaatttggcagataaccattgggcaaaaacttgtgagggcgaaggtcgt
attgaatggtgttgtagtgtatgcagagaatatttccaaaatggtgggaagagaaaagca
cttgaaaaagatgaaaaaagagctgtactcgccactaagaccactccagccttaaattca
catgagtcttctaaacttgaagaccataatgccttgaaattagaactaaatcacaacaag
aagtttggaaggacctcaaacacgtggaggttaaggaccatcctgctaaaagatgaaagg
gtcaaccaggaaattaaggaagaattaaaaagattcatggaaaccaatgagaatgaagat
aaaaccgttcaaaatctttgggatgtagcaaaagcagtcctaagggggaaatacatcaca
atacaagcatccattcaaaaactgctgtttggaaagatagaaagagatggagtacttcca
aattcgttctatgaggccagcatcaccttaattccaaaaccagacaaagaccccaccaaa
aaggagaattacagaccaatatccctgatgaacatggatgtaaaaattctcaacaagata
ctagccaataggatccaacagcacattaagaaaattattcaccacgaccaagtaggattt
attcccgggacacaaggctggttcaacactcgtaaaacaatcagtgtgattcatcatatc
agcaagagaaaaaccaagaaccatatgatcctctcattagatgcagagaaagcatttgac
aaaatacagcatccattcctgatcaaaactcttcagagtgtagggatagagggaacattc
ctcgacatcttaaaagccatctacgaaaagcccacagcaaatatcattctcaatggggaa
gcactgggaacctttcccctaagatcaggaacaagacagggatgtccactctcaccacta
ctattcaacatagtactggaagtcctagcctcagcaatcagacaacaaaaagacataaaa
ggcattcaaattggcaaagaagaagtcaaactctccctcttcgctgatgacatgatactc
tacatagaaaacccaaaagtctccaccccaagattgctagaactcatacagcaatttggt
agcgtggcaggatacaaaatcaatgcccagaaatcagtggcatttctatacactaacaat
gagactgaagaaagagaaattaaggagtcaatcccatttacaattgcacccaaaagcata
agatacctaggaataaacctaaccaaagatgtaaaggatctataccctcaaaactataga
acacttctgaaagaaattgaggaagacacaaagagatggaaaaatattccatgctcaggg
attggcagaattaatattgtgaaaatgtcaatgttacccagggcaatatacacgtttaat
gcaatccctatcaaaataccatggactttcttcagagagttagaacaaattattttaaga
tttgtgtggaatcagaaaagaccccgaatagccagggaattttaa
>NW_876258.1|GENSCAN_predicted_peptide_3|380_aa
MSSTTRSPSLPTTGPRAPCSPSHQVRPISSTASVYAGMGGSGSQTSISCSTSFPGGWRSG
GPAAGMAGGLAGIGGIQGKKETMQDLSDRLASYLERVRRLEADNQRLEMKIREHLEKKGL
PVKYEMELAMRQSVESDIHGLRKVIDDTNVTRLHLETEIEALKEELLFMKKNHEQVKGLQ
NQIANSGLTVELDAPKSQGLSKIMADDKLAQKNWKELDKYWSQQIKESTTVVTTQTSEIG
EAEMTLMELRCTTQSLKINLDSMRNLKSSLENSLREVKACYVMQMEQLNGILLHLESELS
QTRAEGQLQAQEYEALLNVKVKLEAEIATDCRLLEDGEDFSLTDALDNSNSLQTIQKTTT
RKIVDGKVVSETNDTKILRH
>NW_876258.1|GENSCAN_predicted_CDS_3|1143_bp
atgagctccaccacccgctccccttctcttccaactacgggtccccgggctccgtgcagt
cccagccaccaggtccggcccatcagtagcacagccagcgtctatgcaggcatggggggc
tcgggctcccagacctccatatcctgctccaccagcttcccgggtggctggaggtccgga
ggcccggccgcggggatggctgggggtctggcgggcatagggggcatccagggcaagaag
gagaccatgcaagacctgagtgaccgcctggcctcctacctggagagggtgaggagactg
gaggctgataatcagagactggagatgaaaatccgggaacacctggagaagaaggggctc
ccagtcaagtatgagatggagcttgccatgcgccagtctgtggagagtgacatccatggg
ctccgcaaggtcattgatgacaccaacgtcactcggctgcacctagagacagagatcgag
gctctcaaggaggagctgctcttcatgaagaagaaccacgagcaagtaaagggcctacaa
aaccaaatcgccaactctgggttgacggtggagttggatgcccccaaatctcagggcctc
agcaagatcatggcagatgacaagctggctcagaagaactggaaggagctggacaagtac
tggtcccagcagatcaaggaaagcaccacagtggtcaccacacagacctctgagatcgga
gaagctgagatgaccctcatggagttgagatgcaccacccagtccttgaagatcaacctg
gactccatgagaaacctgaagtccagcttggagaacagcctgagggaggtcaaggcctgc
tatgtgatgcagatggagcagctcaacgggatcctgctgcacctggagtcagagctgtcc
cagacccgggcagaggggcagctccaggcccaggagtatgaggccctgctgaatgtcaag
gtcaagctggaggctgagattgccactgactgtcgcctgttggaagacggggaggacttc
agtcttactgacgccctggacaacagcaactccttgcagactatccagaagaccacaacc
cgcaagatcgtggacggcaaggtggtgtctgagaccaacgacacaaaaattctgaggcat
tga
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.