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