GENSCAN 1.0	Date run: 16-Jun-106	Time: 19:15:11

Sequence Pan_troglodytes_annotation_chunk_6 : 92926 bp : 37.47% 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..
----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------

 1.01 Init +   3927   3988   62  2  2   92   36   134 0.941   7.37
 1.02 Intr +   4295   4782  488  2  2   -4   58   251 0.141   4.63
 1.03 Term +  32450  32922  473  0  2   98   33   360 0.767  25.61
 1.04 PlyA +  33658  33663    6                               1.05

 2.04 PlyA -  33984  33979    6                               1.05
 2.03 Term -  39050  39042    9  2  0  131   43     0 0.557  -2.98
 2.02 Intr -  40145  39946  200  0  2   56   93   174 0.799  12.85
 2.01 Init -  42084  42015   70  0  1   62   89    27 0.801   1.46
 2.00 Prom -  52533  52494   40                              -3.75

 3.00 Prom +  52584  52623   40                              -6.75
 3.01 Init +  58969  58982   14  0  2  104   39    13 0.757  -2.67
 3.02 Intr +  59502  59755  254  0  2  122   98   132 0.940  13.75
 3.03 Intr +  63568  63807  240  2  0   93   80   193 0.996  15.60
 3.04 Intr +  65961  66168  208  1  1   96   64   166 0.960  12.21
 3.05 Intr +  68207  69743 1537  2  1   48   16  1534 0.649 130.73
 3.06 Term +  79333  79395   63  0  0   94   38    40 0.023  -3.49
 3.07 PlyA +  79573  79578    6                               1.05

 4.02 PlyA -  81420  81415    6                               1.05
 4.01 Sngl -  85953  85666  288  0  0   55   32   280 0.901  14.44
 4.00 Prom -  89332  89293   40                             -10.05

 5.03 PlyA -  89902  89897    6                               1.05
 5.02 Term -  90253  90017  237  1  0   44   40   279 0.702  13.88
 5.01 Intr -  90956  90594  363  2  0   60   27   530 0.635  38.56

Predicted peptide sequence(s):


>Pan_troglodytes_annotation_chunk_6|GENSCAN_predicted_peptide_1|340_aa
MAWRGRGGLGSEGAGSPGALDLEGQLFAPPHPLERRAPSREHDENLEIAFRASDLAGPAA
ISSTVLGASASLCGVGWHTLASSFPSVPQPFGGRGGGGGLCADPGAGNPTLRLRKPRKSS
PSLSQTLDSSAPGLRRHSEKLLVNLIPEAVPGRGGGGGLTHRLGSSESDATWAQDLSGLE
SELGSFEDGLAALEIWRSDATMRTHTRGAPSVFFIYLLCFVSAYITDENPEVMIPFTNAN
YDSHPMLYFSRAEVAELQRRAASSHEHIAARLTEAVHTMLSSPLEYLPPWDPKDYSARWN
EIFGNNLGALAMFCVLYPENIEARDMAKDYMERMAAQPSW

>Pan_troglodytes_annotation_chunk_6|GENSCAN_predicted_peptide_2|92_aa
MNTKIQGIREERRPGAGGILQRPGLCGISNDLAPDYGISSCAVQNSHVDTGKEKERWMRE
TVVSVAEMCSLNGHGRRRRRSKKAILKIPKGT

>Pan_troglodytes_annotation_chunk_6|GENSCAN_predicted_peptide_3|771_aa
MVMTKLVKDAPWDEVPLAHSLVGFATAYDFLYNYLSKTQQEKFLEVIANASGYMYETSYR
RGWGFQYLHNHQPTNCMALLTGSLVLMNQGYLQEAYLWTKQVLTIMEKSLVLLREVTDGS
LYEGVAYGSYTTRSLFQYMFLVQRHFNINHFGHPWLKQHFAFMYRTILPGFQRTVAIADS
NYNWFYGPESQLVFLDKFVMRNGSANWLADQIRRNRVVEGPGTPSKGQRWCTLHTEFLWY
DASLKSVPPPDFGTPTLHYFEDWGVVTYGSALPAEINRSFLSFKSGKLGGRAIYDIVHRN
KYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAVSKSC
FSPWVGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNV
QRNLILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQRDGLY
KMYWMDDTGYSKKATFASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPSIDVQSF
TVHGDSQQLDVFIATSKHAYATYLWTGEATGQSAFAQVIADHHKILFDRNSVIKSSIVPE
VKDYAAIVEQNLQHFKPVFQLLEKQILSRVRNTASFRKTAERLLRFSDKRQTEEAIDRIF
AISQQQQQQSKSKKNRRAGKRYKFVDAVPDIFAQIEVNEKKIRQKAQILAQKELPIDEDE
EMKDLLDFADVTYEKHKNGGLIKGRFGQARMVVEVNGVIVKRFQSADQCFI

>Pan_troglodytes_annotation_chunk_6|GENSCAN_predicted_peptide_4|95_aa
MVKKKISDSESDDSKSKKKTDAADKPRGFARGLDPERIIGATDSSGELMFLMKWKDSDEA
DLVLAKEASMKCPQIVIAFYEERLTWHSCPEDEAQ

>Pan_troglodytes_annotation_chunk_6|GENSCAN_predicted_peptide_5|199_aa
SEEPGDRELEAGEQNPGAPGEEGTPGQRLEPLLHDHQDLRAQIFTNTVDNARIVLQINAC
FAAVDFSVKYETELAMCQSVESDIHGVHKVIDDTNVTRLQLETEIKALKKQLLFMKNHEE
EMEQLNGILLHLESELAQTQAEGQHQAQEYEALLNIKVKLEAEIATYNNLLEDGEDFNLG
DALDNSNSMQTIQKTPPAQ


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.