GENSCANW output for sequence 12:27:44



GENSCAN 1.0	Date run: 10-Mar-105	Time: 12:27:57

Sequence hg16_dna : 100000 bp : 33.21% 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..
----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------

 1.03 PlyA -    663    658    6                               1.05
 1.02 Term -  60062  59598  465  2  0   -8   41   368 0.800  16.53
 1.01 Init -  60609  60076  534  0  0   49  -29   557 0.492  33.00


Click 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):


>hg16_dna|GENSCAN_predicted_peptide_1|332_aa
MRARSMDRAAVARVGAVVSASVCALVAGVVLAQYIFTLKRKTGRKTKIIEMMPEFQKSSV
RIKNLTRVEEMICGLIKGGAAKLQIITDFDMTLSRFSYKGKRCPTCHNSIDNCQLITDEC
RKKLLQLKKKYYAIEVDPVLTVEEKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDKD
MKNFFDKLQQHSIPVFIFSAGISDVLEEVIRQAGVYHPNVKVVSNFMDFDETGVLKGFKG
VLIHIFNKHDGALRNTEYFNQLKDNSNIILLGDSQGDLRMADGVANVEHILKVGYLNDRV
DELLEKYMDSYDIVLVQDESLEVANSILQKIL


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.