You can find an explanation of each column here:

http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html

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)

The important columns are the first 5 which relate to the coordinates (position) of each exon and the exon type. Further information about the exon and the confidence with which genscan is predicting it can be found in the later columns.

You can find an explanation of each column here:

http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html

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)

The important columns are the first 5 which relate to the coordinates (position) of each exon and the exon type. Further information about the exon and the confidence with which genscan is predicting it can be found in the later columns.

Thanks a million.

Column Description

------ -------------------------------------------------------------

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 "absolute reading frame" relative to start of sequence.

For example, if nucleotides 1,2,3 of the sequence are read as a codon, that's

called reading frame 0. If 2,3,4 are read as a codon, that's reading frame 1.

If 3,4,5 are read as a codon, that's reading frame 2, and so on.

This information, together with the starting and ending positions of the exon,

is sufficient to give the amino acid sequence encoded by the exon.

Another use of the reading frame is that if you see two adjacent predicted exons

separated by a relatively short intron which share the same reading frame,

it may be worth looking at the possibility that the intervening intron is

not correct, i.e. that the two exons plus the intervening intron might form one

long exon (assuming there are no inframe stops in the intron, of course).

Ph "net phase" of exon (exon length modulo 3)

For example, an exon of length 15 bp has net phase 0 since 15 is divisible

by 3, an exon of length 16 bp has net phase 1 because 16 divided by 3 leaves a

remainder of 1, an exon of length 17 bp has net phase 2, and an exon of length

18 bp has net phase 0 again. The point of this is that exons whose net phase

is 0 can be omitted from the gene without disrupting the reading frame: such

exons are candidates for being either 1) incorrect, or 2) alternatively

spliced.

I/Ac initiation signal or acceptor splice site score (x 10)

(If below zero, probably not a real acceptor site.)

Do/T donor splice site or termination signal score (x 10)

(If below zero, probably not a real donor site.)

CodRg coding region score (x 10)

Low coding region scores may indicate potentially incorrect predictions

or genes with unusual amino acid and/or codon usage patterns.

P probability of exon (sum over all parses containing exon)

This quantity is close to the actual probability that the predicted exon

is correct.

Tscr exon score (depends on length, I/Ac, Do/T and CodRg scores)

An overall measure of exon quality based on local sequence properties

http://globin.bx.psu.edu/dist/cathy/piptools.test/genscan.out

Thanks, find it useful