GENSCAN 1.0	Date run:  7-Dec-102	Time: 07:55:25

Sequence 07:55:23 : 19862 bp : 48.86% 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 Intr +    692    928  237  1  0   46  100    59 0.297   0.71
 1.02 Intr +   3136   3172   37  0  1   93  103    10 0.722   0.84
 1.03 Intr +   7078   7166   89  2  2   85   99    94 0.969   9.89
 1.04 Intr +   7447   7573  127  0  1   44   82   191 0.942  14.35
 1.05 Term +  10496  11565 1070  0  2   37   48  1051 0.777  88.29
 1.06 PlyA +  14323  14328    6                               1.05

 2.02 PlyA -  14746  14741    6                               1.05
 2.01 Term -  18920  18091  830  0  2   54   32   725 0.898  56.71

Predicted peptide sequence(s):


>07:55:23|GENSCAN_predicted_peptide_1|519_aa
AGDAGAHVLRPRTVVGRFRTFVASRGRSRPAPAAKDPRVPRQRSRSLPSPPASRPESANH
REARTSHFPRQNKWALGVRGLTSKKEGKNQAALPSKVPAFSDKDSLGDEMLAAALLKAKS
QELVTFEDVAVYFIRKEWKRLEPAQRDLYRDVMLENYGNVFSLDRETRTENDQEISEDTR
SHGVLLGRFQKDISQGLKFKEAYEREVSLKRPLGNSPGERLNRKMPDFGQVTVEEKLTPR
GERSEKYNDFGNSFTVNSNLISHQRLPVGDRPHKCDECSKSFNRTSDLIQHQRIHTGEKP
YECNECGKAFSQSSHLIQHQRIHTGEKPYECSDCGKTFSCSSALILHRRIHTGEKPYECN
ECGKTFSWSSTLTHHQRIHTGEKPYACNECGKAFSRSSTLIHHQRIHTGEKPYECNECGK
AFSQSSHLYQHQRIHTGEKPYECMECGGKFTYSSGLIQHQRIHTGENPYECSECGKAFRY
SSALVRHQRIHTGEKPLNGIGMSKSSLRVTTELNIREST

>07:55:23|GENSCAN_predicted_peptide_2|276_aa
XCRLSTQHEESADEQKGSEAEGLKGDIISVIIANKPEASLERQCVNLENEKGTKPPLQEA
GSKKGRESVPTKPTPGERRYICAECGKAFSNSSNLTKHRRTHTGEKPYVCTKCGKAFSHS
SNLTLHYRTHLVDRPYDCKCGKAFGQSSDLLKHQRMHTEEAPYQCKDCGKAFSGKGSLIR
HYRIHTGEKPYQCNECGKSFSQHAGLSSHQRLHTGEKPYKCKECGKAFNHSSNFNKHHRI
HTGEKPYWCHHCGKTFCSKSNLSKHQRVHTGEGEAP


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.