GENSCAN 1.0 Date run: 16-Jun-106 Time: 19:12:52 Sequence Pan_troglodytes_annotation_chunk_5 : 82926 bp : 38.29% 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.. ----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------ 1.05 PlyA - 8 3 6 1.05 1.04 Term - 3895 3315 581 2 2 -8 37 364 0.345 15.36 1.03 Intr - 4315 4276 40 1 1 90 78 75 0.347 3.58 1.02 Intr - 9829 9727 103 0 1 51 99 80 0.493 4.66 1.01 Init - 16609 16584 26 1 2 68 90 57 0.666 2.34 1.00 Prom - 18674 18635 40 -8.75 2.00 Prom + 39226 39265 40 -6.45 2.01 Init + 41359 41409 51 0 0 64 83 12 0.338 -0.40 2.02 Intr + 50168 50329 162 1 0 77 84 244 0.998 22.15 2.03 Intr + 52351 52444 94 0 1 31 110 103 0.999 5.42 2.04 Intr + 52941 53006 66 1 0 82 116 8 0.656 0.96 2.05 Intr + 53515 53666 152 2 2 74 105 91 0.993 8.36 2.06 Intr + 54959 55165 207 1 0 120 39 185 0.993 15.15 2.07 Intr + 58031 58135 105 1 0 66 99 67 0.966 5.09 2.08 Intr + 60237 60418 182 2 2 82 59 157 0.999 9.94 2.09 Intr + 61489 61582 94 1 1 25 94 92 0.986 2.55 2.10 Intr + 62034 62090 57 2 0 107 115 -10 0.763 1.76 2.11 Intr + 66812 66888 77 1 2 93 86 44 0.988 2.09 2.12 Term + 67485 67662 178 0 1 98 48 138 0.793 6.98 2.13 PlyA + 70653 70658 6 1.05Click 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):
>Pan_troglodytes_annotation_chunk_5|GENSCAN_predicted_peptide_1|249_aa
MGMSRKAQRCRWQQRSHRKWDAACGLRDWLLCVLLAVDPVTPQGEAEEDGTELEPGALKP
VVNLVNALQNIWKKNKHLKDLETLMVELCVVFQSKNAWTVIGKGGKNIKAFCIDYRARVL
APEGNGPKCMLSISADIETIGEILKKIIPTLEEYHHYKGSNFDCELRLLTHQSLAGGIIE
VKDAKIKELQENTQTTIKLFQECCPHSTDGVVLIGERLWSCRVHKIILNLISESPTEDVH
RLITPIFMM
>Pan_troglodytes_annotation_chunk_5|GENSCAN_predicted_peptide_2|474_aa
MATSGAPALQWVAGQQEHKDAYQVILDGVKGGTKEKRLAAQFIPKFFKHFPELADSAINA
QLDLCEDEDVSIRRQAIKELPQFATGENLPRVADILTQLLQTDDSAEFNLVNNALLSIFK
MDAKGTLGGLFSQILQGEDIVRERAIKFLSTKLKTLPDEVLTKEVEELILTESKKVLEDV
TGEEFVLFMKILSGLKSLQTVSGRQQLVELVAEQADLEQTFNPSDPDCVDRLLQCTRQAV
PLFSKNVHSTRFVTYFCEQVLPNLGTLTTPVEGLDIQLEEYMPLPPEEAENGENAGNEEP
KLQFSYVECLLYSFHQLGRKLPDFLTAKLNAEKLKDFKIRLQYFARGLQVYIRQLRLALQ
GKTGEALKTEENKIKVVALKITNNINVLIKDLFHIPPSYKSTVTLSWKPVQKVEIGQKRA
SEDTTSGSPPKKSSAGPKRDARQIYNPPSGKYSSNLGNFNYGERFRLGTRNMRD
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.