GENSCAN 1.0	Date run: 13-Mar-108	Time: 11:34:24

Sequence panTro2_dna : 113620 bp : 37.94% 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..
----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------

 1.03 PlyA -   1018   1013    6                               1.05
 1.02 Term -   4627   3701  927  1  0   44   41   691 0.647  51.16
 1.01 Init -   5434   5069  366  1  0  104   87   335 0.981  32.07
 1.00 Prom -  15261  15222   40                              -8.15

 2.00 Prom +  23920  23959   40                              -3.95
 2.01 Init +  27519  27607   89  2  2   38  101    47 0.096   1.16
 2.02 Intr +  43684  43814  131  1  2   26   49   112 0.050   0.52
 2.03 Intr +  70135  70318  184  2  1  137   17   168 0.089  12.52
 2.04 Intr +  70753  71044  292  1  1   -7  -15   476 0.097  24.01
 2.05 Intr +  83244  83370  127  2  1   69  106   154 0.958  14.63
 2.06 Intr +  87034  87192  159  2  0   41   93   157 0.986  10.54
 2.07 Term +  88179  89698 1520  1  2  130   39   710 0.889  59.97
 2.08 PlyA +  90779  90784    6                               1.05

Predicted peptide sequence(s):

Predicted coding sequence(s):


>panTro2_dna|GENSCAN_predicted_peptide_1|430_aa
MEELVTEKEAEESHRPDSVSLLTFILLLTLTILTIWLFKYCRVHFLHETGLAMICGLIVG
VILRYGTPGTRGRDKLLNCTQEDQAFSTLVVDVSGKFFEYTLKREISPGKINSVKQNDML
GKSVGIFLGIFSGCFTMGAVTGVVTALVTKFTKLDCFPLLETALFFLMSWSTFLLAEACG
FTGVVAVLFCGITQAHYTFNNLLVESRSRSKQLFEAENFIFSCMVLALFTFQKHVFSPVF
IIGAFVAVFLGRAAHIYPLSFFLSLGRRHKIGWNFQHTMMFSGLRGAVAFALAICDTASY
ARQMTFTTTPFIVFFTIWIIGGGTTPMLSWLNIRVSIKEPSKEDRNEHHWQYFRVGVDPD
QDPPPNNDSFQVLQGDSPDSARGNWTKQESTWIFRLWYSFDHNYLKPILTHSGSPLTTTL
PPGGDTAAPH

>panTro2_dna|GENSCAN_predicted_CDS_1|1293_bp
atggaggagctcgtcactgagaaggaggcggaagagagccaccggccagacagtgtgagc
ctgctcaccttcatcctgctgctcacgctcaccatcctcaccatatggctcttcaagtac
tgccgggtgcactttctgcatgagaccgggctggccatgatctgtgggctcatcgttggg
gtgatcctgaggtatggtacccctggcaccaggggccgtgacaaattactcaactgcact
caagaagatcaggccttcagcactttagtagtggatgtcagcggtaaattcttcgaatac
actctgaaaagagaaatcagccctggcaagatcaacagcgtaaagcagaatgacatgcta
gggaagtcagttggcatttttctaggtatatttagtggctgttttaccatgggagctgtg
actggtgttgtgactgctttagtgaccaagtttaccaaactggactgctttcccctgctg
gagacggcgctcttcttcctcatgtcctggagcacgtttctcttggcagaagcctgcgga
tttacaggcgttgtagctgtccttttctgtggaatcacacaagctcattacaccttcaac
aatctgttggtggaatcaagaagtcgaagcaagcagctctttgaggcagagaacttcatc
ttctcctgcatggtcctggcgctatttaccttccagaagcacgttttcagccctgttttc
atcattggagcttttgttgctgtcttcctgggcagagccgcccatatctacccgctctcc
ttcttcctcagcttgggcagaaggcataagattggctggaattttcaacacacgatgatg
ttttcaggcctcaggggagcagtggcatttgcgttggccatctgtgacacggcatcctat
gctcgccagatgacgttcaccaccacgcctttcatcgtgttcttcaccatctggatcatt
ggaggaggcacgacacccatgttgtcatggcttaatatcagagttagcatcaaggagccc
tccaaagaggaccgcaacgaacaccactggcagtacttcagagttggtgttgaccccgat
caagatccaccacccaacaatgacagctttcaagtcttacaaggggacagcccagattct
gccagaggaaactggacaaaacaggagagcacatggatattcaggctgtggtacagcttt
gatcacaattacctgaagcccatcctcacacacagcggctccccgctaaccaccactctc
ccgcctggtggagacacagcggctccccactaa

>panTro2_dna|GENSCAN_predicted_peptide_2|833_aa
MQPRTYVDLKLAFCDCNGKQIKQEEDVGRCLRTECQRARGCGSPGPFVPHTGASVCLKAR
QISKAINRDRSAGGLAFGEGKAAATLGASVSREEERPSQGSSHWRGIRRVRRRSTPETKA
ASQAGGGRGNGAQKQSKRAGVSGGGKGCGEGASQIPEMPEFLEDPSVLTKDKLKSELVAN
NVTLPAGEQRKDVYVQLYLQHLTARNRPPLPAGTNSKGPPDFSSDEEREPTPKATKKTDK
PRQEDKDDLDVTELTNEDLLDQLVKYGVNPGPIVGTTRKLYEKKLLKLREQGTESRSSTP
LPTISSSAENTRQNGSNDSDRYSDNEEGKKKEHKKVKSTRDTVPFSELGTTPSGGGFFQG
ISFPEISTRPPLGSTELQAAKKVHTSKGDLPREPLVATNLPGRGQLQKLASERNLFISCK
SSHDRCLEKSSSSSSQPEHSAMLVSTAASPSLIKETTTGYYKDIVENICGREKSGIQPLC
PERSHISDQSPLSSKRKALEESESSQLISPPLAQAIRDYVNSLLVQGGVGSLPGTSNSMP
PLDVENIQKRIDQSKFQETEFLSPPRKVPRLSEKSVEERDSGSFLAFQNIPGSELMSSFA
KTVVSHSLTTLGLEVAKQSQHDKIHASELSFPFHESILKVIEEEWQQVDRQLPSLACKYP
VSSREATQILSVPKVDDEILGFISEATPLGGIQAASTESCNQQLDLALCRAYEAAASALQ
IATHTAFVAKAMQADISQAAQILSSDPSRTHQALGILSKTYDAASYICEAAFDEVKMAAH
TMGNSTVGRRYLWLKDCKINLASKNKLASTPFKGGTLFGGEVCKVIKKRGNKH

>panTro2_dna|GENSCAN_predicted_CDS_2|2502_bp
atgcagccaagaacatatgttgacctaaaactggcattctgtgattgtaatggaaaacag
ataaagcaggaggaagatgtaggaagatgcctgaggactgaatgccaaagggccaggggg
tgtgggtcaccaggaccctttgttcctcacactggggctagtgtttgcctcaaagctaga
cagatcagtaaagctattaaccgggataggtcagcaggtgggctagcgtttggggaaggc
aaggctgcggctactcttggagcttcagtgtcccgggaggaagaaaggcccagccaaggg
tcctcacactggcgtggaattcggcgcgttcgtaggcgatcgaccccagagacgaaagct
gcttctcaagctgggggagggagaggaaacggcgcacaaaagcagagcaagcgcgccggc
gtgagcggcggcggcaaaggctgtggggagggggcttcgcagatccccgagatgccggag
ttcctggaagacccctcggtcctgacaaaagacaagttgaagagtgagttggtcgccaac
aatgtgacgctgccggccggggagcagcgcaaagacgtgtacgtccagctctacctgcag
cacctcacggctcgcaaccggccgccgctccccgccggcaccaacagcaaggggcccccg
gacttctccagtgacgaagagcgcgagcccaccccgaaagccacaaaaaaaactgataaa
cccagacaagaagataaagatgatctagatgtaacagagctcactaatgaagatcttttg
gatcagcttgtgaaatacggagtgaatcctggtcctattgtgggaacaaccaggaagcta
tatgagaaaaagcttttgaaactgagggaacaaggaacagaatcaagatcttctactcct
ctgccaacaatttcttcttcagcagaaaatacaaggcagaatggaagtaatgattctgac
agatacagtgacaatgaagaaggaaagaagaaagaacacaagaaagtgaagtccactagg
gatactgttcctttttctgaacttggaactactccctctggtggtggattttttcagggt
atttcttttcctgaaatctccacccgtcctcctttgggcagtaccgaactacaggcagct
aagaaagtacatacttctaagggagacctacctagggagcctcttgttgccacaaacttg
cctggcaggggacagttgcagaagttagcctctgaaaggaatttgtttatttcatgcaag
tctagccatgataggtgtttagagaaaagttcttcgtcatcttctcagcctgaacacagt
gccatgttggtctctactgcagcttctccttcactgattaaagaaaccaccactggttac
tataaagacatagtagaaaatatttgcggtagagagaaaagtggaattcaaccattatgt
cctgagaggtcccatatttcagatcaatcgcctctctccagtaaaaggaaagcactagaa
gagtctgagagctcacaactaatttctccgccacttgcccaggcaatcagagactatgtc
aattctctgttggtccagggtggggtaggtagtttgcctggaacttctaactctatgccc
ccactggatgtagaaaacatacagaagagaattgatcagtctaagtttcaagaaactgaa
ttcctgtctcctccacgaaaagtccctagactgagtgagaagtcagtggaggaaagggat
tcaggttcctttttggcatttcagaacatacctggatccgaactgatgtcttcttttgcc
aaaactgttgtctctcattctctcactaccttaggtctagaagtggctaagcaatcacag
catgataaaatacatgcctcagaactatcttttcccttccatgaatctattttaaaagta
attgaagaagaatggcagcaagttgacaggcagctgccttcactggcatgcaaatatcca
gtttcttccagggaggcaacacagatattatcagttccaaaagtagatgatgaaatccta
gggtttatttctgaagccactccactaggaggtattcaagcagcctccactgagtcttgc
aatcagcagttggacttagcactctgtagagcatatgaagctgcagcatcagcattgcag
attgcaacccacactgcctttgtagctaaggctatgcaggcagacattagtcaagctgca
cagattcttagctcagatcctagtcgtacccaccaagcgcttgggattctgagcaaaaca
tatgatgcagcctcatatatttgtgaagctgcatttgatgaagtgaagatggctgcccat
accatgggaaattccactgtaggtcgtcgatacctctggctgaaggattgcaaaattaat
ttagcttctaagaataagctggcttccactccctttaaaggtggaacattatttggagga
gaagtatgcaaagtaattaaaaagcgtggaaataaacactag


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.