GENSCAN 1.0	Date run: 16-Jul-101	Time: 04:24:55

Sequence D_gene : 4350 bp : 41.56% 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 +    368   2279 1912  0  1   95   89  1449 0.984 137.07
 1.02 Intr +   2327   2571  245  2  2   65   92   203 0.830  19.62
 1.03 Intr +   2753   2997  245  0  2   72   61   284 0.972  25.39
 1.04 Term +   3082   3912  831  0  0   71   45   883 0.996  79.32
 1.05 PlyA +   4122   4127    6                               1.05

Predicted peptide sequence(s):


>D_gene|GENSCAN_predicted_peptide_1|1077_aa
XLELLKKKEEDNTMLFFLFFFYLLLSSSSDLVFADRRVLHEPFFPIDSPPPSPPSPPPLP
KLPFSSTTPPSSSDPNASPFFPLYPSSPPPPSPASFASFPANISSLIVPHATKSPPNSKK
LLIVAISAVSSAALVALLIALLYWRRSKRNQDLNFSDDSKTYTTDSSRRVYPPPPATAPP
TRRNAEARSKQRTTTSSTNNNSSEFLYLGTMVNQRGIDEQSLSNNGSSSRKLESPDLQPL
PPLMKRSFRLNPDVGSIGEEDEEDEFYSPRGSQSGREPLNRVGLPGQNPRSVNNDTISCS
SSSSGSPGRSTFISISPSMSPKRSEPKPPVISTPEPAELTDYRFVRSPSLSLASLSSGLK
NSDEVGLNQIFRSPTVTSLTTSPENNKKENSPLSSTSTSPERRPNDTPEAYLRSPSHSSA
STSPYRCFQKSPEVLPAFMSNLRQGLQSQLLSSPSNSHGGQGFLKQLDALRSRSPSSSSS
SVCSSPEKASHKSPVTSPKLSSRNSQSLSSSPDRDFSHSLDVSPRISNISPQILQSRVPP
PPPPPPPLPLWGRRSQVTTKADTISRPPSLTPPSHPFVIPSENLPVTSSPMETPETVCAS
EAAEETPKPKLKALHWDKVRASSDREMVWDHLRSSSFNENVVVEIMNVVCRLDEEMIETL
FVAKSLNNKPNQSQTTPRCVLPSPNQENRVLDPKKAQNIAILLRALNVTIEEVCEALLEG
NADTLGTELLESLLKMAPTKEEERKLKAYNDDSPVKLGHAEKFLKAMLDIPFAFKRVDAM
LYVANFESEVEYLKKSFETLEAACEELRNSRMFLKLLEAVLKTGNRMNVGTNRGDAHAFK
LDTLLKLVDVKGADGKTTLLHFVVQEIIRAEGTRLSGNNTQTDDIKCRKLGLQVVSSLCS
ELSNVKKAAAMDSEVLSSYVSKLSQGIAKINEAIQVQSTITEESNSQRFSESMKTFLKRA
EEEIIRVQAQESVALSLVKEITEYFHGNSAKEEAHPFRIFLVVRDFLGVVDRVCKEVGMI
NERTMVSSAHKFPVPVNPMMPQPLPGLVGRRQSSSSSSSSSTSSSDEDEHNSISLVS


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.