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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggactctctgtctctttgtgttctgttcttggttgtagaagtttgaagtgttttttggtataagtcgtttcattctttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT

Basic information

species Vitis vinifera
transcript Vv08s0040g02640.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g02640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 6
gtacggactctctgtctctttgtgttctgttcttggt-tgtagaagtttgaagtgttttttggtataagtcgtttcattctttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT
||| | |  ||   |   |   || |  ||  |   | | ||     |||| |  |||    | || | | |||  || | | |||| ||||||||||||||||||||||||||||||||||||||||| ||||| 
gtaagcaaactactttcgtcattgctaagtcttgactctttattgagttgatggattt----gcatgaatggttctatgcct-gcagCTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA

upper sequence: Vv08s0040g02640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 4
gtacggactctctgtctctt-tgtgttctgttcttggttgtagaagtttgaagtgttttttggtataagtcgtttcattctttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT
||| | | | |   |||||| | |    | ||  |  || |      |||| |  |||    | ||   | |||  || | | |||||||||||||||||||||| ||||||||||||||||||||||||||||| 
gtaagaaatttacctctcttgtttcacttattgatccttttgttgagttgatggattt----gcatcgatggttctatgcct-gcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA

upper sequence: Vv08s0040g02640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G33100.1 (Glycine max), 3'ss of exon 4
gtacggactctctgtctctttgtgttctgttcttggttgtagaagtttgaagtgttttttggtataagtcgtttcattctttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT
||| ||  ||| |   |  |||| ||   || ||||||||||| | |  ||| | || | ||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
gtaagggttcttt--ttggttgtctttctttattggttgtagatgctaaaagagattgt-ggtataagtggtttcattctttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT

upper sequence: Vv08s0040g02640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G35800.1 (Glycine max), 3'ss of exon 2
--------------------------------gtacggactctctgtctctttgtgttctgttcttggttgtagaagtttgaagtgttttttggtataagtcgtttcattctttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT
                                |   | |    ||         |||| | |  ||||||||||| | |  ||| |  | ||| ||||||| ||||||||||||||||||||||||| |||||||||||||||||||||| ||||||||||||||||
gtaagggttctttctgattctctttcattattggttgtagatgctaaaagagaatgttgtata-ttggttgtagatgctaaaagagaatgttg-tataagtggtttcattctttgcagTTGTGTGCAGATACGGAATTGGTTTGACTATCTTAATCATATTTGTATT

upper sequence: Vv08s0040g02640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G53570.4 (Arabidopsis thaliana), 3'ss of exon 6
gtacggactctctgtctctttgtgttctgttcttggttgtagaagtttgaagtgttttttggtataagtcgtttcattctttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT
||| | | | | | | || |  |  | | |  | | | ||   | ||| |  |    |||||||||||   ||  |||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
gtaagaa-tatttctttcctcttactatttcttcgctagttttaatttta--ttacatttggtataagcttttcaattccttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT

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|352774223|gb|FQ474746.1|FQ474746
EST:     GAAATTGATGTGCTACAGAAGCTTGCCAGGCATGATGTTGGAGGCACTCG                         TTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT
genomic: GAAATTGATGTGCTACAGAAGCTTGCCAGGCATGATGTTGGAGGCACTCGgtacggactc ... ttctttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT
EST: gi|352789724|gb|FQ476322.1|FQ476322
EST:     GAAATTGATGTGCTACAGAAGCTTGCCAGGCATGATGTTGGGGGCACTCG                         TTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT
genomic: GAAATTGATGTGCTACAGAAGCTTGCCAGGCATGATGTTGGAGGCACTCGgtacggactc ... ttctttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT
EST: gi|71860081|gb|DT009136.1|DT009136
EST:     GAAATTGATGTGCTACAGAAGCTTGCCAGGCATGATGTTGGAGGCACTCG                         TTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT
genomic: GAAATTGATGTGCTACAGAAGCTTGCCAGGCATGATGTTGGAGGCACTCGgtacggactc ... ttctttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggttgtagaagtttgaagtgttttttggtataagtcgtttcattctttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT
                                     tcgtttcattcttt  CT-rich tract
                     tgtttttt  TA-rich tract