GENSCAN 1.0 Date run: 6-Apr-102 Time: 02:22:19 Sequence 02:22:18 : 2963 bp : 38.44% C+G : Isochore 1 ( 0 - 43 C+G%) Parameter matrix: Arabidopsis.smat Predicted genes/exons: Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr.. ----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------ 1.01 Intr + 744 1091 348 2 0 89 83 157 0.558 14.93 1.02 Intr + 1183 1378 196 0 1 73 54 211 0.792 19.27 1.03 Intr + 1590 1643 54 1 0 66 70 33 0.597 2.33 1.04 Intr + 1815 1875 61 1 1 53 77 37 0.952 0.97 1.05 Intr + 1972 2041 70 1 1 99 60 88 0.999 10.37 1.06 Term + 2176 2463 288 0 0 45 42 247 0.814 15.19 1.07 PlyA + 2664 2669 6 -1.75Click 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):
Predicted coding sequence(s):
>02:22:18|GENSCAN_predicted_peptide_1|338_aa
ARPSVSTVPRDRITVAHVSGEGQRQECPVETHSLQLINQPQEQKIMTWSSDQIRGFFDFP
VPDPQAASSRTMVSSKEVLSKCEWPDWADQLISDDSLEPNWSELLGDPNVLNLYSKIETQ
SSDIARQEIVFRNQHQVDPSMEPFNAKSPPASSMTSKQRMRWTPELHEAFVEAINQLGGS
EPHLKRLYIIGLSRNTELQEEPLVKNLKTIEDIKSLDLKTSIEITEALRLQMKVQKQLHE
QLEIQRSLQLQIEEQGRYLQMMIEKQQKMQENKKDSTSSSSMPEADPSAPSPNLSQPFLH
KATNSEPSITQKLQNGSSTMDQSESTSGTSNRKRVRED
>02:22:18|GENSCAN_predicted_CDS_1|1017_bp
gcacggccatctgtttctaccgtgccaagagacagaattactgttgctcacgtctctggt
gaagggcagaggcaggaatgccctgtggaaacacattccttgcaattgatcaatcaacct
caagaacagaaaattatgacttggtcttcagaccagattcggggcttcttcgattttcct
gttccagatccacaagcagcgagcagcagaactatggtttcatccaaggaagtgctttca
aaatgcgaatggccagactgggcggatcagttgatctctgatgatagtcttgaaccaaat
tggtcggagcttctaggtgatcctaatgtactcaatctatattcaaagatagaaacacag
tcttctgatatagcaaggcaagagatcgtctttagaaatcagcatcaggtggatccatca
atggagccgtttaatgccaaaagcccaccagctagttcaatgacatctaagcaaagaatg
cgttggacaccagaacttcatgaagcatttgtcgaagctatcaatcagctcggtggtagt
gaacctcatcttaaacgtctttatattattggcttgtccagaaatacagaactgcaagaa
gaacctctagtaaagaatttgaaaaccattgaagatatcaaatctcttgacttgaagacg
agcattgaaatcactgaagctctccggttacagatgaaagttcaaaaacaactccacgag
caacttgagatccaaagatcactgcagttacaaatcgaagaacaaggtcggtatcttcag
atgatgattgagaaacaacagaagatgcaagagaacaaaaaagactctacttcctcatca
tcaatgccagaagctgacccttcagctccatcaccaaacctttcacaacctttcctccat
aaagcaaccaattcagaaccatcaataactcagaaactgcagaatggttctagcacaatg
gatcaaagtgaatctacttctgggactagtaatagaaaacgggttagagaagattag
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.