GENSCAN 1.0 Date run: 11-Nov-99 Time: 16:44:23 Sequence genomic : 3864 bp : 61.98% C+G : Isochore 4 (57 - 100 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 + 1884 2070 187 2 1 85 84 314 0.986 28.07 1.02 Term + 3217 3362 146 2 2 48 42 185 0.983 8.92 1.03 PlyA + 3416 3421 6 1.05Click here to view a gif image of the predicted gene(s)
Click here for a PostScript image of the predicted gene(s)
Predicted peptide sequence(s):
>genomic|GENSCAN_predicted_peptide_1|110_aa
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAED
LQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
Explanation
Gn.Ex : gene number, exon number (for reference)
Type : Init = Initial exon
Intr = Internal exon
Term = Terminal exon
Sngl = Single-exon gene
Prom = Promoter
PlyA = poly-A signal
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 codon ending at x is in frame f = x mod 3)
Ph : net phase of exon (length mod 3)
I/Ac : initiation signal or acceptor splice site score (x 10)
Do/T : donor splice site or termination signal score (x 10)
CodRg : coding region score (x 10)
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. Thus, for example, a predicted donor splice site with
score > 100 is excellent; 50-100 is acceptable; 0-50 is weak; and
below 0 is poor (probably 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. This information can be used to assess the reliability of the
predicted exon, e.g., it would be better to design PCR primers based on
a predicted exon with probability > 0.95 than one with lower probability.