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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctctatgcccccttttttttttatcatattcttagctaaaattgcaaaactgatactttctggataaag

Basic information

species Vitis vinifera
transcript Vv13s0019g04480.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04480.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os04g43750.1 (Oryza sativa), 5'ss of exon 9
GTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctctatgcccccttttttttttatcatattcttagctaaaattgcaaaactgatactttctggataaag--------------------------------------------------------------------------------------------------------
|| || |||||||||||||||||||| || || ||||||||||||   |||   || ||||| ||||| |||| ||  ||  |  ||  | | |  |||| |||        | | || | | |    |   |   |  | ||                                                                                                          
GTGTTTATGATGAACCTTTCTGCTCCCTTTATATGTGAATTCTTCCGTGATGCCCAAGAGAAGGCTCTTCCgtgagtactgggttccactatatgcttattataaataactttgacatagaacattcaacgttgcattaacaactgcagcacattattcttctaaacccatgcacttcatccatgttagaatttttccaatacagtgctatgtaaaacaggattaaagttcttttgatcaccaaactag

upper sequence: Vv13s0019g04480.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA19G36630.1 (Glycine max), 5'ss of exon 9
GTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagc-tctatgcccccttttttt---tttatcatattcttagctaaaattgcaaaactgatactttctggataaag
 |||||   ||||||||||||||||| || |||||||| || |||| ||||  |||||||||||||||||||||||  || || |||  |   ||    |  || |  || | |  |    |   ||   ||    ||    |||  ||
ATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACCgtaaggatccatccccaataaattaaaatgaataaatttttcatatttgttcttaaggatgcccattatgtgatttag

upper sequence: Vv13s0019g04480.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 9
GTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctctatgcccccttttttttttatcat---attcttagctaa-aattgcaaaactgatactttctggataaag
 |||||||||||||||||||||| ||||| |||||||| ||||||||||||  || | | |||| ||| |||||||     | | |  ||   ||   |  |    | | |||  ||   ||   || | ||    |||  ||||  ||
TTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGATGCACTGAATAAAGTTCTGCCgtaaggatccttctctgttaaattcaaagaaagaaaattttacatattgatcttaataatgtccattttgggattcag

upper sequence: Vv13s0019g04480.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA03G33910.3 (Glycine max), 5'ss of exon 6
GTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctctatgcccccttttttttttatcatattcttagctaaaattgcaaaactgatactttctggataaag
 |||||   |||||||||||||| || || ||||| || || |||| ||||  |||||||||||||||||||||||    || |  | |        |   || ||      |     |  |  |   | | | | ||  | |  
ATCTTCTCAATGAACCTTTCTGCCCCTTTTATCTGCGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACCgtaagg---attcatcttaaaacgaatgaaattttacatattggttcttaaggatgcacattatgtgatttag-

upper sequence: Vv13s0019g04480.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA10G06580.1 (Glycine max), 5'ss of exon 9
GTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctctatgcccccttttttttttatca----tattcttagctaaaattgcaaaactgatactttctggataaag
 ||||||||||||||||||||||||| || || ||||| ||||| |||| |  || ||| |||| ||| |||||||     | |    ||   |||  |  |     ||| |        ||   || | || |  ||   ||||  ||
ATCTTCATGATGAACCTTTCTGCTCCCTTTATATGTGAGTTCTTTAAGGGTGCACTGGACAAAGTTCTGCCgtaaggatccttctttgttaaatttgaagaaagaaaattatacatattgatcttaataatgttcattctgggattcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110418987|gb|EC985176.1|EC985176
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|110687648|gb|EE065296.1|EE065296
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAACAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|110728204|gb|EE103570.1|EE103570
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGGAGCAAGAACCTTTGCCAA
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|351023138|gb|FQ432521.1|FQ432521
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|351023529|gb|FQ432912.1|FQ432912
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|351038074|gb|FQ460816.1|FQ460816
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|352794243|gb|FQ479485.1|FQ479485
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|352786944|gb|FQ475977.1|FQ475977
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|110693709|gb|EE070177.1|EE070177
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACANGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|349824265|gb|FQ417652.1|FQ417652
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTGCCAA
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|352794240|gb|FQ479482.1|FQ479482
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|110391898|gb|EC956929.1|EC956929
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|351028349|gb|FQ427245.1|FQ427245
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAACTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTTCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|110708040|gb|EE085129.1|EE085129
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAAATGAA-CGGAAGCAAGAACCTTTGCCA
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAA-TGAAACGGAAGCAAGAACCTTTTCCA
EST: gi|110399344|gb|EC965847.1|EC965847
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|351013485|gb|FQ425516.1|FQ425516
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAA-CAAGAAACTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|110703696|gb|EE080770.1|EE080770
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGNAAGCAAGAACCTTTGCCAA
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|30302319|gb|CB979113.1|CB979113
EST:     ATTCTTC-AGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: ATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|27581929|gb|CB004624.1|CB004624
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|351026422|gb|FQ428434.1|FQ428434
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|110689258|gb|EE065335.1|EE065335
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTGCCAA
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|30125628|gb|CB910967.1|CB910967
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTA
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTA
EST: gi|83275808|gb|DV939816.1|DV939816
EST:     AAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: AAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|351038237|gb|FQ460929.1|FQ460929
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|110685346|gb|EE063661.1|EE063661
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|110685881|gb|EE062990.1|EE062990
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|30129600|gb|CB914939.1|CB914939
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAA
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAA
EST: gi|110726165|gb|EE101710.1|EE101710
EST:     CTCCATTCATCTGTGAATTCTTTCA-GGATCAACAAGAGAAAGCTCTACC                         GTACATGGATTATGTAATTGGGAAATGAAAC
genomic: CTCCATTCATCTGTGAATTCTT-CAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAA-TGAAAC
EST: gi|110715240|gb|EE093065.1|EE093065
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACG-AAGCAAGAACCTTTGCCAA
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|110698283|gb|EE075646.1|EE075646
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|22013186|gb|BQ798220.1|BQ798220
EST:     CCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: CCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
EST: gi|32245795|gb|CD711614.1|CD711614
EST:     GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC                         GTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG
genomic: GCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctcta ... ctggataaagGTACATGGATTATGTATTTGGGAATGAAACGGAAGCAAGAACCTTTTCCAG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACCgtaagctctatgcccccttttttttttatcatattcttagctaaaattgcaaaactgatactttctggataaag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA