GENSCAN 1.0	Date run:  2-Apr-107	Time: 22:00:30

Sequence chunk2-7 : 80323 bp : 40.96% 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 Sngl +   6288   7220  933  2  0   84   54   957 0.999  88.10
 1.02 PlyA +   8927   8932    6                               1.05

 2.03 PlyA -  10182  10177    6                               1.05
 2.02 Term -  18802  17553 1250  2  2    9   32   960 0.152  73.25
 2.01 Init -  36038  35879  160  2  1   91   72   262 0.757  24.93
 2.00 Prom -  36186  36147   40                             -17.34

 3.00 Prom +  36292  36331   40                             -17.61
 3.01 Sngl +  36374  37033  660  1  0   77   48   782 0.516  69.02
 3.02 PlyA +  37598  37603    6                               1.05

 4.06 PlyA -  40034  40029    6                               1.05
 4.05 Term -  41098  40661  438  1  0  -17   53   401 0.861  20.39
 4.04 Intr -  41527  41213  315  1  0  -28   61   530 0.932  34.04
 4.03 Intr -  41899  41631  269  2  2  111   42   287 0.697  22.73
 4.02 Intr -  77852  77657  196  2  1   31   57   136 0.140   2.87
 4.01 Init -  78129  77992  138  0  0   49   33   283 0.999  17.09

Predicted peptide sequence(s):


>chunk2-7|GENSCAN_predicted_peptide_1|310_aa
MNALTKVKLINKLNEGEVQLGVADKVSWHSEYKDSAWIFLGGLPYELTEGDIICVFSQYG
EIVNINLVRDKKTGKSKGFCFLCYEDQRSTILAVDNFNGIKIKGRTIQVDHVSNYQAPKN
SEEMDDATKELQKGSYGPHTYSSSSSESSEDEQPIKKHKKEKKEKKKRKKEKEKTDRLVQ
AEQPSSSSPTSKTVKEKDDPGPKKHSSKNSERTQKSQPRERRKLPEARTAYYGGAEDLER
ELKKEKRKHEHKSSSRKEAREETTGDRDRGQSSDTLSSPYNWRSEGRSHRTRSRSQDKSH
RHKKARRSWE

>chunk2-7|GENSCAN_predicted_peptide_2|469_aa
MPWCHDEGEDSPGDTIACKASLAYARAIVEYESSDVVMHGELAAAVDGRQRGEVFCFPSV
LMASSAKSAEMPTISKTLNPTPDPHQEYLDPRITIALFEIGSHSPSSWGSLPSLKNSSHQ
VTEQQTAQKFNNLLKEIKDILKNMAGFEEKITEAKELFEETNIPEDVSAHKENIRGLDKI
NEMLSTNLPVSLAPEKEDNEKKQEMILETNITEDVSAHKENIRGLDKINEMLSTNLSLSL
APEKEDNEKKQEMIMENQNSENTVQVFARDLVNRLEEKKVLNETQQSQEKAKNRLNVQEE
TMKIRNNMEQLLQEAEHWSKQHTELSKLIKSYQKSQKDISETLGNNGVDFQTQPNNEVSA
KHELEEQVKKLSHDTYSLQLMAALLENECQILQQRVEILKELHHQKQGTLQEKPIQINYK
QDKKNQKPSEAKKVEMYKQNKQEMKGTFQKKDRSCRSLDACLNKKACNT

>chunk2-7|GENSCAN_predicted_peptide_3|219_aa
MGSPTLCPSMKGTPLPHTILCLDLAGRNLTDYLMKILTQCGYSFTATVMQEIVCDIKKKL
CCIPLDFEQETAMVGSSSSLEKSYKLPNGQVITISNKWFCCPEALFQTSFVGMESCGIHE
TTFNSIMKSDVDIYKDLYANAVLSGSTTMYPSITNRMQKEITALAPSAMKIKITAPPECK
YSVWIRGSILASLSTFQQMWISKQEYNKSGPSIVHGKCF

>chunk2-7|GENSCAN_predicted_peptide_4|451_aa
MPKARSLAPRAARALLAASRLERWAQPRLTLERRSASAERLGAEAWAGGLLRSLPGWGAE
LRSRPPAFGPHAPGLVRGLAALGPSPNESAAPLRLRIRRKSLLLPLKGWSLNSMSFTTRS
TTSSTNYWSLGSVQLPSYVAQLVSSVVSVYAGAGGSGFRISVSHSTSFWGGLGDLVGIGD
IQNEKETMQGLNDCLASYLDRTIEDLRVQIFASTVDSACIILQIDKAHITADDFRVKCET
ELAMCQSVESDIHGLRKSTDDTNVTQLQLEAEIEALKEELLFMKKTHEEEVKGLQAQIAS
SGLTMETEESTKQSAEIGASEIMLMELRHTLQSLEINLNSMRNLKARLENSLREVETRYA
MQMEQLNRVQLHLKLKLAQTWAEGQHQVQEYEALLNIKIKLEAEITTYHHLLEDEEGFNP
GDALDSSNSIQSIQKTTTHRIVDSIGGPPGV


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.