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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgttttcacttatactatgttagaaagttttctttacttaatgaactgttatggtagcccttaattattcatataaagcatttattgtacttctcatcagctttcttttacacagGTATATCCTATGTACAAGGCTTTTATTGAGCCAGATCTACAAACAGCACATATAAAAATCATCAACAAATTCAATCCATTCACTGGATTTCAGAACCCCA

Basic information

species Vitis vinifera
transcript Vv17s0000g04650.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g04650.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 4
--------------------------------gtgt-tttcacttatactatgtta----gaaagttttctttacttaatgaactgttatggtagccctta-attattcatataaagcatttattgtacttctcatcagctttcttttaca--------------------cagGTATATCCTATGTACAAGGCTTTTATTGAGCCAGATCTACAAACAGCACATATAAAAATCATCAACAAATTCAATCCATTCACTGGATTTCAGAACCCCA
                                 ||  |||| | |||  | ||||      |||| | |   |||  |   |||  | ||        ||| ||| |  || || || || | ||  |     |||| |  || ||| |||                    ||||| ||||| ||||| |||||||| |||||||||||  | || ||||||||||||||||| |||||||| ||||| |||||| | || || || || || |
gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaaagatcttaatacaaaccaaacattcatttcgcaatttatattttgtatgtatagtatctttttcatc---catctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA

upper sequence: Vv17s0000g04650.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G143804_T01 (Zea mays), 3'ss of exon 1
------------------------------------------gtgttttcacttatactatg---ttagaaagttttctttacttaat-gaactgttatggtagcccttaattattcatataaagcatttattgtactt--------ctcatcagctttcttttacacagGTATATCCTATGTACAAGGCTTTTATTGAGCCAGATCTACAAACAGCACATATAAAAATCATCAACAAATTCAATCCATTCACTGGATTTCAGAACCCCA
                                           | | |  |   |||   ||   ||   || ||  ||||||  | | | |    | | || |  | |  | |     |    ||  ||| |||| ||         | ||||    |    |    |||| ||||  |||||||||||||| || || |||||| |||| || |||||||| |||||||| ||||| ||||| |||| | | || || || || || |
gtacaacgagctagccaggaacccgaagaaataattgatcaaatctctcaaacgataggttgaaatttccaacttggctttacacattaggagcaatcttgtggttcatgttaacagtgaattggctcttactgtaattggtgtggtttaatcaaagatgacatttttagGTTTATCTAATGTACAAGGCTTTCATCGAACCAGATTTACAGACCGCACATATTAAAATCATTAACAAGTTCAACCCATGCTCAGGTTTCCAAAATCCTA

upper sequence: Vv17s0000g04650.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 4
gtgttttcacttatactatgttagaaagttttctttacttaatga-actgtt--atggtagcccttaattattcatataaagcatttattgtacttctcatcagctttcttttacacagGTATATCCTATGTACAAGGCTTTTATTGAGCCAGATCTACAAACAGCACATATAAAAATCATCAACAAATTCAATCCATTCACTGGATTTCAGAACCCCA
||   || | || | | |  |    |    || | |    ||||    |||    || || |  | |||||    | ||  | | ||  |||  ||      |   |    ||   ||||| ||||| |||||||||||||| || || |||||| |  | || |||||||| || ||||||||||| ||||| |||||  | || || || || || |
gtaggttgaattttccaacttggctatacattttatgagcaatgttgttgtccattgttaacagtgaattacctct-tactgtaattggtgtggtttaatgaaatatgacatttttcagGTTTATCCAATGTACAAGGCTTTCATCGAACCAGATTTGGAGACCGCACATATTAAGATCATCAACAAGTTCAACCCATTTTCAGGGTTCCAAAATCCTA

upper sequence: Vv17s0000g04650.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G07610.1 (Glycine max), 3'ss of exon 5
gtgttttcacttatactatgttagaaagttttctttacttaatgaactgttatggtagcccttaattattcatataaagcatttattgtacttctcatcagct------ttcttttacacagGTATATCCTATGTACAAGGCTTTTATTGAGCCAGATCTACAAACAGCACATATAAAAATCATCAACAAATTCAATCCATTCACTGGATTTCAGAACCCCA
|| |||||||| || | ||||||||    ||| ||  ||| | ||   ||| ||  | |    |  | |      || |||  |  | || |||| | |   |      ||   ||    |||| ||||||||||| || |||||||| ||||||||||| |||||||| ||| ||||||| || ||||| || ||||||||| ||||||||||||| ||||
gt-ttttcactgatcccatgttaga----tttgttgtctttagga---gttttgaaaacttgcatctttaagaccaaggcacctgctataattcttaactattattgtgtttccttttgtagGTGTATCCTATGTATAAAGCTTTTATCGAGCCAGATCTCCAAACAGCCCATTTAAAAATTATTAACAAGTTTAATCCATTCTCTGGATTTCAGAATCCCA

upper sequence: Vv17s0000g04650.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G09080.1 (Glycine max), 3'ss of exon 4
gtgttttcacttatactatgttagaaagttttctttactt--aatgaactgttatggtagcccttaattattcatataaagcatttattgtacttctcatcagctttcttttacacagGTATATCCTATGTACAAGGCTTTTATTGAGCCAGATCTACAAACAGCACATATAAAAATCATCAACAAATTCAATCCATTCACTGGATTTCAGAACCCCA
|| |||||||| ||   |||||| ||  ||||    ||||   |  |  ||     |||   || |   |      || |   ||||    |||  |  |  | || ||||| ||  ||| ||||||||||| || ||||||||||||||||||||  ||||||| ||| ||||||| || ||||| || ||||||||| ||||||| ||||| ||||
gt-ttttcactgatctcatgttataatttttttaggacttttgaaaacttgcatctgtaagactaaggcacctgc-tataattttta----actattgttttgtttccttttgca--gGTGTATCCTATGTATAAAGCTTTTATTGAGCCAGATCTCAAAACAGCTCATCTAAAAATTATTAACAAGTTTAATCCATTCTCTGGATTCCAGAATCCCA

upper sequence: Vv17s0000g04650.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G73980.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------------------------gtgttttcacttatactatgttagaaagttttctttacttaatgaac-tgttatggtagccctta-----attattcatataaagcatttatt-------gtacttctcatcagctttcttttaca--cagGTATATCCTATGTACAAGGCTTTTATTGAGCCAGATCTACAAACAGCACATATAAAAATCATCAACAAATTCAATCCATTCACTGGATTTCAGAACCCCA
                                                      || | |||    | || | |      | ||    ||   ||  ||| ||  | | |  | | ||     | |     | |  ||  ||| ||         | ||  | |  | ||| || | ||  ||||| ||||||||||||||||| |||||||| || |||||  | ||||| || || || ||| | || || ||||| ||||||| ||| ||||||||||| |
gttttcatgctagtctttgctatcttttattttttagcccagattaatcacccttgctgtcatgcctgctgtttggagttgcttcaaatatggaaaaaacatgaaacgatgtctcctactcctactggatgttttgagtttttttttacagtaaaattttgcttatgtttttttctccaaccagGTTTATCCTATGTACAAGGCGTTTATTGAACCTGATCTGAAGACAGCTCAGATTAAGATCCTTAATAAGTTCAACCCATTCAGTGGCTTTCAGAACCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattattcatataaagcatttattgtacttctcatcagctttcttttacacagGTATATCCTATGTACAAGGCTTTTATTGAGCCAGATCTACAAACAGCACATATAAAAATCATCAACAAATTCAATCCATTCACTGGATTTCAGAACCCCA
 ccttaat  putative branch site (score: 4)
                                        ctttcttttac  putative PPT
     tattcatataaagcat  TA-rich tract