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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctctattacatctctttatttggttgattttttcttctggtttcttgtatactccctagacaaattctctttaaaagttttcatagggattcaaaattttcaagattgagtttgttcctttctcccttcctctttgtgaaaccatatattgcttggttgtagGTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTTTCATCACCACAGTCAAGGCTAGCTG

Basic information

species Vitis vinifera
transcript Vv03s0038g02200.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g36670.1 (Oryza sativa), 3'ss of exon 5
--------------gttctctattacatctctttatttggttgattttttcttctggtttcttgtatactccctagacaaattctctttaaaagttttcatagggattcaaaattttcaagattgagtttgttcctttctcccttcctctttgtgaaacc--atatattgcttggttgtagGTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTTTCATCACCACAGTCAAGGCTAGCTG
               | ||| |||   |     | | |  || |  |||  || ||  || |  | ||   |  ||    |   | ||      | | ||| | |  | | | ||||  | |||   | ||  |  | | |   | ||  || |    |    | |  ||      || ||||||| || ||||||  ||||| ||||||||||| ||||| || ||||||| ||| |||||| ||||| | |||||
gtcagaaattcagaatgctcaattgatttgtactttctactttacctttatttatgagttat-atgtatcgctaagttgcacatttttctcc--tatacatggagcat-agatttttagatattctttatgcgctctgccctgcttctgattatctctcttggtctgctgtcatcatgcagGTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTTACATTACCACAATCAAGACAAGCTG

upper sequence: Vv03s0038g02200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G371271_T01 (Zea mays), 3'ss of exon 10
gttctctattacatctctttatttggttgattttttcttctggtttcttgtatactccctagacaaattctctttaaaagttttcatagggattcaaaattttcaagattgagtttgttcctttctcccttcctctttgtgaaaccatatattgcttggttgtagGTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTTTCATCACCACAGTCAAGGCTAGCTG
                                             || || ||      | ||     |||  | | | || |  ||         |||||||  | |||  | | ||   || |  |  | | | |  |           |||||   ||| ||| |||||| | |||| |||||| |||| |||||||||||| |||||||||| ||| || ||  ||||| | |||||
-------------------------------------------aatcatgaatgggtgtttga-----tcttctgacaggtatctat------ctgaaattttttaaattaggatggtcatttccaactctacccctgct-----------ttgctgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG

upper sequence: Vv03s0038g02200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G158237_T05 (Zea mays), 3'ss of exon 4
gttctctattacatctctttatttggttgattttttcttctggtttcttgtatactccctagacaaattctctttaaaagttttcatagggattcaaaattttcaagattgagtttgttcctttctcccttcctctttgtgaaaccatatattgcttggttgtagGTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTTTCATCACCACAGTCAAGGCTAGCTG
                                             || || ||      | ||     |||  | | | || |  ||  | |||      |||  | |||  | | ||   || |  |  | | | |  |           |||||   ||| ||| |||||| | |||| |||||| |||| |||||||||||| |||||||||| ||| || ||  ||||| | |||||
-------------------------------------------aatcatgaatgggtgtttga-----tcttctgacaggtatctatctgaatt------tttttaaattaggatggtcatttccaactctacccctgct-----------ttgctgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG

upper sequence: Vv03s0038g02200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G03540.1 (Glycine max), 3'ss of exon 5
gttctctattacatctctttatttggttgattttttcttctggtttcttgtatactccctagacaaattctctttaaaagttttcatagggattcaaaattttcaagattgagtttgttcctttctcccttcctctttgtgaaaccatatattgcttggttgtagGTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTTTCATCACCACAGTCAAGGCTAGCTG
                       ||  | |   |||  | ||| |    | ||  || ||  |  | |  | |||  |    || ||     |     ||||  ||||| | |||||     ||           | | | ||| | ||  |  | || ||| |||||||||||| ||||  ||||||||||||||||| |||||||| ||||||||| | |||||||| ||||| || ||
----------------------gtgagtaacaatttgct-tggatgaaagcat-ttcgctttattattaatatttttataacttgatgtttttctgtcatttctaagat-gtgtttgagttgtt-----------tctataaaatcttac-tcccatgattgcagGTGTTGTTTCTATGGCAAATTCAGGACCTGATTCCAATGGCTCACAGTTTTTCTTTACCACAGTGAAGGCCAGATG

upper sequence: Vv03s0038g02200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G11370.1 (Glycine max), 3'ss of exon 5
gttctctattacatctctttatttggttgattttttcttctggtttcttgtatactccctagacaaattctctttaaaagttttcatagggattcaaaattttcaagat-tgagtttgttcctttctcccttcctctttgtgaaaccatatattgcttggttgtagGTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTTTCATCACCACAGTCAAGGCTAGCTG
                       ||  | |   |||  | ||| |    | ||  ||  |  |  | |  | |||  |    || ||     |     ||||  ||||| || |||||     ||           | | ||||| | ||  |  | || ||| ||| |||||||| ||||  ||||||||||||||||| |||||||| ||||||||| | |||||||| ||||| || ||
----------------------gtgagtaacaatttgct-tggatgaaagcat-ttcattttattattaatatttttataacttgatgtttttctgtcatttctaagatatgtgtttGAGTTGTT-----------TCTATGAAATCTTAC-TCCCATGATTGCAGGAGTTGTTTCTATGGCAAATTCAGGACCTGATTCCAATGGCTCACAGTTTTTCCTTACCACAGTGAAGGCCAGATG

upper sequence: Vv03s0038g02200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G00580.1 (Glycine max), 3'ss of exon 5
gttctctattacatctctttatttggttgattttttcttctggttt-cttgtatactccctagacaaattctctttaaaagttttcatagggattcaaaattttcaagattgagtttgttcctttctcccttcctctttgtgaaaccatatattgcttggttgtagGTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTTTCATCACCACAGTCAAGGCTAGCTG
                                | |    | | | | |||| || |       | || ||   |||  ||      |||      ||   || |  |  ||     ||| |  ||   |  |  ||  ||| || |    || ||||  |||| |||||| || || |||||||||||||| |||||||| |||||||| |||||||| || || ||||| ||| |    ||
-------------------------------gtctgtaacagatatgcttggatgc------aagaattttaattttgaaaaaaaaataacttgacatttttctttatttttgaggtgtacgattaagctgtt-tccctgtaaatc----tactgctctgttgcagGTGTAGTCTCTATGGTGAATTCAGGTCCTGATTCCAATGGCTCACAGTTTTTTATTACAACAGTGAAGACCGCTTG

upper sequence: Vv03s0038g02200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G00650.1 (Glycine max), 3'ss of exon 6
gttctctattacatctctttatttggttgattttttcttctggtttcttgtatactccctagacaaattctctttaaaagttttcatagggattcaaaattttcaagattgagtttgttcctttctcccttcctctttgtgaaaccatatattgcttggttgtagGTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTTTCATCACCACAGTCAAGGCTAGCTG
               ||| ||   | |    ||        | ||| |  | |  ||  || | ||| |  ||| | |  |||         ||||   ||||  || |   ||  |||    |     |   ||  ||| ||    |||| | |   |||| |||||| || || |||||||||||||| || ||||  |||||||| |||||||| || |||||||| ||| |  | ||
--------------gtctgtaacagatatgcttggatgcaagctttttacttttttctttaaaaaaaataacttcacatttttc--------ttca---tttttgaggt---gtacgtttaagt-----tgtttccatgtaaa----tatacttcactgttgcagGTGTAGTCTCTATGGTGAATTCAGGTCCCGATTACAATGGCTCACAGTTTTTTATTACCACAGTGAAGACCGGTTG

upper sequence: Vv03s0038g02200.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G34960.1 (Arabidopsis thaliana), 3'ss of exon 4
gttctctattacatctctttatttggttgattttttcttctggtttcttgtatactccctagacaaattctctttaaaagttttcatagggattcaaaattttcaagattgagtttgttcctttctcccttcctctttgtgaaaccatatattgcttggttgtagGTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTTTCATCACCACAGTCAAGGCTAGCTG
                       ||      |   |  | |      || |  | |     ||  |||| |     ||| |  |  ||| |       |||||    |   | |||     |      |||  | ||  |   |  ||  |||   |   ||||||| | ||  | ||||  ||| ||||||| |||||||||||||| ||||| || ||||| || || |||||||||||
----------------------gtgcgcatatacatactttaccaatttatgaatttt---gaagaattgttccggaaaatggttttagagc------attttgcgcaagcaatttacgtata-----cttgttgttcataggaaaatgaattttgtatgtgtagGTATGGTAGCAATGGCTAATACAGGACCGGATTCTAATGGCTCGCAGTTCTTTATCACTACTGTTAAGGCTAGCTG

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|110385283|gb|EC949792.1|EC949792
EST:     TGGTGGCACATTTCGAGATGAGAATTTCAGGATAAAACATTCACATGCAG                         GTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTT
genomic: TGGTGGCACATTTCGAGATGAGAATTTCAGGATAAAACATTCACATGCAGgttctctatt ... ttggttgtagGTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTT
EST: gi|351021974|gb|FQ437761.1|FQ437761
EST:     TGGTGGCACATTTCGAGATGAGAATTTCAGGATAAAACATTCACATGCAG                         GTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTT
genomic: TGGTGGCACATTTCGAGATGAGAATTTCAGGATAAAACATTCACATGCAGgttctctatt ... ttggttgtagGTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTT
EST: gi|110380524|gb|EC945796.1|EC945796
EST:     TGGTGGCACATTTCGAGATGAGAATTTCAGGATAAAACATTCACATGCAG                         GTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTT
genomic: TGGTGGCACATTTCGAGATGAGAATTTCAGGATAAAACATTCACATGCAGgttctctatt ... ttggttgtagGTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtttgttcctttctcccttcctctttgtgaaaccatatattgcttggttgtagGTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTTTCATCACCACAGTCAAGGCTAGCTG
                                    atatatt  TA-rich tract