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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctataatccattagttaatatagttaatttttgttatgttttggtcaactatttgaaggttacatcaatgcttatttgcaatattctgatcagaaaattgagcttgctaaaccctgcagGTTGAAATCAACGACGTACCTTCAGATACTAAGGATAAGGATGAGATTCTGGAGAGTGAATTCTTTGACACCAGACAGGCATTTCTGAGTCTTTGTCAAG

Basic information

species Vitis vinifera
transcript Vv09s0054g01780.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 14
gtaagttctataatccattagttaatatagttaatttttgttatgttttggtcaactatttgaaggttacatcaatgcttatttgcaatattctgatcagaaaattgagcttgctaaaccctgcagGTTGAAATCAACGACGTACCTTCAGATACTAAGGATAAGGATGAGATTCTGGAGAGTGAATTCTTTGACACCAGACAGGCATTTCTGAGTCTTTGTCAAG
                           ||  | | |    |||| || |  ||   | ||   |         |||  | | |  |  |||          || |||| | | | | ||  |  ||||||| ||    |   | ||   |||||| |||||||  ||||| |||||||| |||||||| ||||||||||| ||||| || || ||||| |||||||
--------------------------gtaactgactgaacttatattctcttc--ttgttgagaaaaggagcaaatagtaactaacg-tat----------aacttgatccttccatacttt--agGTTGACATTGTTGGGTTGCCCAAAGATACCAAGGATAGAGATGATATTCTGGAAAGTGAATTTTTTGACACCAGGCAGGCCTTCCTTAGTCTCTGTCAAG

upper sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os06g49130.1 (Oryza sativa), 3'ss of exon 13
gtaagttctataatccattagttaatatagttaatttttgttatgttttggtcaactatttgaaggttacatcaatgcttatttgcaatattctgatcagaaaattgagcttgctaaaccctgc--agGTTGAAATCAACGACGTACCTTCAGATACTAAGGATAAGGATGAGATTCTGGAGAGTGAATTCTTTGACACCAGACAGGCATTTCTGAGTCTTTGTCAAG
                             || | |  | | ||   ||         |||   || |  ||  || ||      | || ||  | | || |    |    || |  | |  |||  ||||||||||    |  ||  ||  |||||| ||||| |  |||   ||  | || | |||  |||||||||||||||||||||| |||||| |||||||||
-----------------------------gtaagtaatggatagcattcaagttttaattcatagatatcagtaaagcaacagggtaa-ataatcaccaaatctcttttatttcatatcattgcttagGTTGAAATTGTTGGGGTCTCTGAAGATACCAAGGACAGAGATATTATCTTAGAAAATGAGATCTTTGACACCAGACAGGCATTCCTGAGTTTTTGTCAAG

upper sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 13
gtaagttctataatccattagttaatatagttaatttttgttatgttttggtcaactatttgaaggttacatcaatgcttatttgcaatattctgatcagaaaattgagcttgctaaaccctgcagGTTGAAATCAACGACGTACCTTCAGATACTAAGGATAAGGATGAGATTCTGGAGAGTGAATTCTTTGACACCAGACAGGCATTTCTGAGTCTTTGTCAAG
                                      |  |||    |  |||    | | |   |   |  |  ||  ||     | | ||| |  | |  | |    |  ||      |  ||||||| ||    |  || ||   |||||| || ||||  ||||| ||  |||| ||||| ||||||||||||||||||||||| || |||||||| ||||
-------------------------------------gtactatacccttttcat---tctcagtatagaactagagcaaat-----agactctcaagatatgactcgattctctctgtttt--agGTTGATATTCTTGGGGTGCCCAAAGATACCAAAGATAGAGATGACATCTTGGAAAGTGAGTTCTTTGACACCAGACAGGCATTCCTTAGTCTTTGCCAAG

upper sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 16
gtaagttctataatccattagttaatatagttaatttttgttatgttttggtcaactatttgaaggttaca--tcaatgcttatttgcaatattctgatcagaaaattgagcttgctaaaccctgcagGTTGAAATCAACGACGTACCTTCAGATACTAAGGATAAGGATGAGATTCTGGAGAGTGAATTCTTTGACACCAGACAGGCATTTCTGAGTCTTTGTCAAG
                 |  |  |  | | | || | ||   ||   |    |||  ||  |   | | ||  |  | |   ||||| ||| || |           | | |||||       ||||||||||||| |  || || ||||| ||||| ||||| || ||||| ||||| ||||| |||||||||||||| |||||||||||||||||||| || || |
----------------ttctgaaagcaaaataaactattcaaatacataca-caatcatacggtagctccaagtataagtgaatttggaatttttt-----------taaacttgcatcttaatgcagGTTGAAATTACTGATGTTCCTTCTGATACAAAGGACAAAGATGATATTCTTGAGAGCGAATTCTTTGACACTAGACAGGCATTTCTGAGTCTCTGCCAGG

upper sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 14
gtaagttctataatccattagttaatatagttaatttttgttatgttttggtcaactatttgaaggt-tacatcaatgc--ttatttgcaatattc-tga---tcagaaaattgagcttgctaaaccctgcagGTTGAAATCAACGACGTACCTTCAGATACTAAGGATAAGGATGAGATTCTGGAGAGTGAATTCTTTGACACCAGACAGGCATTTCTGAGTCTTTGTCAAG
                                 | |||| |||        | | |||||  ||     |||   | ||  |   |   | |||   |||   |  |||  || | | |||   |   ||||||||||||| |  || || ||||| ||||| ||||| || ||||| ||||| ||||| |||||||||||||| |||||||||||||||||||| || || |
---------------------------------acttttcttaaagcaaaataagctattcaaatacacacaatcacgcggtagctccaagtataagtgaattttggaatttttaacgtgcatcatgatgcagGTTGAAATTACTGATGTTCCTTCTGATACAAAGGACAAAGATGATATTCTTGAGAGCGAATTCTTTGACACTAGACAGGCATTTCTGAGTCTCTGCCAGG

upper sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 14
gtaagttctataatccattagttaatatagttaatttttgttatgttttggtcaactatttgaaggttacatcaatgcttatttgcaatattctgatcagaaaattgagcttgctaaaccctgcagGTTGAAATCAACGACGTACCTTCAGATACTAAGGATAAGGATGAGATTCTGGAGAGTGAATTCTTTGACACCAGACAGGCATTTCTGAGTCTTTGTCAAG
 ||| || |  |   ||| | || || |  |  ||| || | ||   |     ||  | |  ||  | | ||      || |  | |   || || ||                       || |||| ||||| |  || |||||| | ||||| ||||| || || |||||||| |||||||||||||||||||| || ||||||||||||||||| || || |
ataaattatggagctcataatttgatgtgatgtattcttttgatagctaa---aatcagtaaaaaatgatattggaattt-tccgtacctttatgttc----------------------ttgtagGTAGAAATTACTGATGTACCTGCCGATACGAAGGACAAAGACGAGATTCTTGAGAGTGAATTCTTTGACACTAGGCAGGCATTTCTGAGTCTCTGCCAGG

upper sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 14
gtaagttctataatccattagttaatatagttaatttttgttatgttttggtcaactatttgaaggttacatcaatgcttatttgcaatattctgatcagaaaattgagcttgctaaaccctgcagGTTGAAATCAACGACGTACCTTCAGATACTAAGGATAAGGATGAGATTCTGGAGAGTGAATTCTTTGACACCAGACAGGCATTTCTGAGTCTTTGTCAAG
|||||||  ||   |  ||  ||    |    || | |    | ||| || |||  ||       ||  |||    | || | |    |||| | |||  ||||   |   || |  |   || ||||||| |||  |||  | ||| | ||||||||||| |  |||||||| || || |||||||||||||| || || || ||||| |||||||| |||||||
gtaagttgcattggc--ttgttttgggtcaggaactgtgacgaggttctg-tcactta-------gtctcat--gcgtttctctattttattgt-atcgcaaaagataatgtgtttgatattgtagGTTGAGATCGCCGATATTCCTACGGATACTAAGGACAGAGATGAGATACTTGAAAGTGAATTCTTTGATACAAGGCAAGCATTCCTGAGTCTATGTCAAG

upper sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaagttctataatccattagttaatatagttaatttttgttatgttttggtcaactatttgaaggttacatcaatgcttatttgcaatattctgatcagaaaattgagcttgc-taaaccctgcagGTTGAAATCAACGACGTACCTTCAGATACTAAGGATAAGGATGAGATTCTGGAGAGTGAATTCTTTGACACCAGACAGGCATTTCTGAGTCTTTGTCAAG
                                    |  |||   ||||      ||  |||| | |    |   |     ||  | ||  || | |  |  |||   | | |  |  |    ||||||||| || |  ||  | ||| ||||||| |  || || ||||| || || || || || || || ||||| ||||| ||||||||||||||||||||||
-----------------------------------gtgagttgcatttt------cttgttgaggatagtgttctttagctttgtctatgatcagttttgtgaatattggtggtattgatatcgcagGTTGAGATTATGGATATTCCTGCAGATACAAGAGACAAAGATGAAATACTCGAAAGCGAGTTTTTCGACACTAGACAAGCATTTCTGAGTCTTTGTCAAG

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|34542459|gb|CF510691.1|CF510691
EST:     NNNNNNNNNNNCATCCTGTCAATCACAGGGACAAACATCTACTCCATCCA                         GTTGAAATCAACGACGTACCTTCAGATACTAAGGATAAGGATGAGATTCTG
genomic: AGAGAGAGAGACATCCTGTCAATCACAGGGACAAACATCTACTCCATCCAgtaagttcta ... aaccctgcagGTTGAAATCAACGACGTACCTTCAGATACTAAGGATAAGGATGAGATTCTG
EST: gi|34549540|gb|CF517772.1|CF517772
EST:     NNNNNNNNNNNCATCCTGTCAATCACAGGGACAAACATCTACTCCATCCA                         GTTGAAATCAACGACGTACCTTCAGATACTAAGGATAAGGATGAGATTCTG
genomic: AGAGAGAGAGACATCCTGTCAATCACAGGGACAAACATCTACTCCATCCAgtaagttcta ... aaccctgcagGTTGAAATCAACGACGTACCTTCAGATACTAAGGATAAGGATGAGATTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatgcttatttgcaatattctgatcagaaaattgagcttgctaaaccctgcagGTTGAAATCAACGACGTACCTTCAGATACTAAGGATAAGGATGAGATTCTGGAGAGTGAATTCTTTGACACCAGACAGGCATTTCTGAGTCTTTGTCAAG
                                        tgctaaa  putative branch site (score: 2)
       ttatttgcaatatt  TA-rich tract