gc_object_start: gene_grailexp --organism human --output pretty --nodb --dbpat grailexp_v3
# Service: gene_grailexp
# Version: 3.3
# Description: GAT GrailEXP Gene Prediction Service
# Last Modified: October, 2001
# Tool: GrailEXP 3.3 from ORNL. Last updated: October, 2001.
# Database: GrailEXP Database Thu Feb 27 16:15:37 EST 2003 from NCBI/TIGR/Baylor/Riken (15960696 entries). Last updated: Thu Feb 27 16:15:37 2003.
# Sequence Name: >gene_grailexp|PID=16092
# Sequence Length: 10686
# Output_begin: pretty
--------------------------------------------------------------------------------
GrailEXP v3.31 [March, 2002] http://compbio.ornl.gov/grailexp/
Authors: Doug Hyatt, Manesh Shah, Victor Olman, Richard Mural, Ying Xu, and
Edward C. Uberbacher, 1996-2001
Reference: "Automated Gene Identification in Large-Scale Genomic Sequences",
Xu, Y. and Uberbacher, E.C., Journal of Computational Biology, Volume 4,
Number 3, 1997
Sequence: >gene_grailexp|PID=16092 (10686 bp)
--------------------------------------------------------------------------------
GAWAIN Gene Predictions (3 predicted, 0 with database similarity)
Genes with Database Similarity (0 predicted, 0 with alternative splices)
Genes with No Database Evidence (3 predicted)
Gene 1, Variant 1 Strand: + Bounds: 715-2833 Exons: 4
Start Codon: Yes Stop Codon: Yes
---Index---- --------Exons-------- ---------CDS--------- -Ph- -Fr- -Len- -Scr-
1.1.1 715 759 715 759 0 0 45 86
1.1.2 1166 1356 1166 1356 0 1 191 100
1.1.3 1426 1537 1426 1537 2 1 112 78
1.1.4 2711 2833 2711 2833 0 1 123 95
Gene 2, Variant 1 Strand: + Bounds: 4015-4809 Exons: 2
Start Codon: Yes Stop Codon: Yes
---Index---- --------Exons-------- ---------CDS--------- -Ph- -Fr- -Len- -Scr-
2.1.1 4015 4116 4015 4116 0 0 102 94
2.1.2 4561 4809 4561 4809 0 0 249 96
Gene 3, Variant 1 Strand: + Bounds: 6470-8915 Exons: 4
Start Codon: Yes Stop Codon: Yes
---Index---- --------Exons-------- ---------CDS--------- -Ph- -Fr- -Len- -Scr-
3.1.1 6470 6730 6470 6730 0 1 261 61
3.1.2 6873 7006 6873 7006 0 2 134 100
3.1.3 7308 7407 7308 7407 2 0 100 100
3.1.4 8781 8915 8781 8915 0 2 135 100
PolyA 9779 9784 ... ... . . 6 90
>GrailEXP Gene 1, Var 1 mRNA
atgggtcagaacctgattctgaacatgaacgatcacggcttcgtggtctgcgcttttaacaggacggttt
ccaaagtggatgactttctggccaatgaggccaaaggaaccaaagtgatcggtgctcacagcctggagga
gatggtctcgaagctgaagaagcctcgacgcatcatcttgctggtgaaggctggaagtgcagtggatgat
ttcatcaataaattagtgaggcagattactgaatctttgagtccggacgaaacgctgatttattttttgc
aggtgccgttgttggagactggagacatcataattgatggtgggaattctgagtatagagataccacgag
acgctgtaaggagctgctgcaaaaaggcctcttatttgttggaagtggtgttagtggtggagaggagggg
gccagatatggtccttcactcatgccaggaggatccaaagaagcctggtaa
>GrailEXP Gene 1, Var 1 protein
MGQNLILNMNDHGFVVCAFNRTVSKVDDFLANEAKGTKVIGAHSLEEMVSKLKKPRRIILLVKAGSAVDD
FINKLVRQITESLSPDETLIYFLQVPLLETGDIIIDGGNSEYRDTTRRCKELLQKGLLFVGSGVSGGEEG
ARYGPSLMPGGSKEAW*
>GrailEXP Gene 2, Var 1 mRNA
atggtgcacaatgggattgaatatggagacatgcagttgatctgtgaggcctaccacctgatgaaagatg
ttgtgggcatggaccacgatgagatgtcacaggtatttgaagaatggaataacactgaactggactcttt
cctgattgaaatcacagccaatattctcaaattcaaagataaggatggcaaatacctcctcccaaagatc
agggacagtgcaggacaaaaaggcacggggaagtggacggcaatttctgccctggaatatggagtccctg
tcactctcataggtaaatggctctttgatcgagccttgtctttcctacctgcacatggcatatcacacta
a
>GrailEXP Gene 2, Var 1 protein
MVHNGIEYGDMQLICEAYHLMKDVVGMDHDEMSQVFEEWNNTELDSFLIEITANILKFKDKDGKYLLPKI
RDSAGQKGTGKWTAISALEYGVPVTLIGKWLFDRALSFLPAHGISH*
>GrailEXP Gene 3, Var 1 mRNA
atgtggctctgtttcactgtgagcagtggctcatcgttcagtggcagtcactgtgtaataggacaagtgt
ctcagatcttaatggtggtactgatcttactaattctattctttcctaccctacccaaaggtgaggctgt
gtttgcacggtgcctgtcgtccctcaaggatgagagagtgcaggccagtaagctgctgaatgggcctaaa
ttgactcaatttagtgggaacaagaaggcatttcttgaggacatacgcaaggccctgtatgcttccaaga
ttatctcctatgctcaaggcttcatgctgctgagacaagcagccaaagaattcggctggacgctgaatta
tggtggcattgcactgatgtggaggggaggctgcatcatcagaagtgtgttcctgggaaaaatcaaagac
gcttttgatcgaaaccctgaacttcagaatttgctgttggatgatttctttaagacagctgtagaaaaat
gccaggactcctggcgacacgtaatcagtactggagtccagcatggtattcctatgccctgcttcactac
agcactttccttttatgatggatacagacatgaagtgctgccagctaacctgatccaggtaggtgcctga
>GrailEXP Gene 3, Var 1 protein
MWLCFTVSSGSSFSGSHCVIGQVSQILMVVLILLILFFPTLPKGEAVFARCLSSLKDERVQASKLLNGPK
LTQFSGNKKAFLEDIRKALYASKIISYAQGFMLLRQAAKEFGWTLNYGGIALMWRGGCIIRSVFLGKIKD
AFDRNPELQNLLLDDFFKTAVEKCQDSWRHVISTGVQHGIPMPCFTTALSFYDGYRHEVLPANLIQVGA*
--------------------------------------------------------------------------------
PERCEVAL Exon Candidates (12 predicted)
Index Std Begin End Frm Type Len Scr Quality
1 + 402 613 0 Internal 212 59 Marginal
2 + 684 759 2 Internal 76 100 Excellent
3 + 1166 1356 0 Internal 191 100 Excellent
4 + 1166 1618 0 Terminal 453 80 Good
5 + 2711 2829 2 Internal 119 98 Excellent
6 + 3986 4116 1 Internal 131 100 Excellent
7 + 4561 4775 0 Internal 215 100 Excellent
8 + 4751 4894 0 Internal 144 87 Good
9 + 6496 6730 2 Internal 235 63 Marginal
10 + 6873 7006 0 Internal 134 100 Excellent
11 + 7308 7407 2 Internal 100 100 Excellent
12 + 8781 8915 0 Terminal 135 100 Excellent
--------------------------------------------------------------------------------
# Output_end: pretty
gc_object_end: gene_grailexp --organism human --output pretty --nodb --dbpat grailexp_v3
gc_object_start: cpg_grailexp --output pretty
# Service: cpg_grailexp
# Version: 3.0
# Description: GAT GrailEXP CpG Island Locator
# Last Modified: December 4, 2000
# Tool: GrailEXP 3.3 from ORNL. Last updated: October, 2001.
# Sequence Name: >cpg_grailexp|PID=30557
# Sequence Length: 10686
# Output_begin: pretty
--------------------------------------------------------------------------------
GrailEXP v3.31 [March, 2002] http://compbio.ornl.gov/grailexp/
Authors: Doug Hyatt, Manesh Shah, Victor Olman, Richard Mural, Ying Xu, and
Edward C. Uberbacher, 1996-2001
Reference: "Automated Gene Identification in Large-Scale Genomic Sequences",
Xu, Y. and Uberbacher, E.C., Journal of Computational Biology, Volume 4,
Number 3, 1997
Sequence: >cpg_grailexp|PID=30557 (10686 bp)
--------------------------------------------------------------------------------
PERCEVAL CpG Islands (1 predicted)
Index Begin End Ratio Pct_GC
1 51 858 0.88 69.92
--------------------------------------------------------------------------------
# Output_end: pretty
gc_object_end: cpg_grailexp --output pretty