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Explanation to understand GENSCAN tool

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).