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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaaatgttgttgaattatgaaggttattgacatgttttatgtgtagtagttttttttctattgctgatttttggtttctcattctgatattatattttcaatttacagCCTAGATGGAGTGATTTAGATGTCAATCAGCATGTTAACAATGTTAAGTACATCGGTTGGATCCTTGAG

Basic information

species Vitis vinifera
transcript Vv11s0016g04480.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os11g43820.1 (Oryza sativa), 3'ss of exon 5
----gtaagtcaaatgttgttgaattatgaaggttattgacatgttttatgtgtagtagttttttttcta---ttgctgatttttggtttc-----tcattc--------tgatattatat---tttcaattta------cagCCTAGATGGAGTGATTTAGATGTCAATCAGCATGTTAACAATGTTAAGTACATCGGTTGGATCCTTGAG
    || ||  | |  | |||  ||  | ||  ||||    |||  | |  || | |  ||| | |   |    |  | || |||| | ||     |||||         |||| ||  ||    |    ||||      |||||||||||| ||||  | ||||||||||||||||| ||||||||||| || || || ||||||||||||
gtaagtcagctagacatagttacatactaaa--ttatcattatgcctcaactgcaatcatttatctaagaaaaatagtaatatttgatctcacccctcatttattttaaatgatctttgatggactcttgtttactgcaacagCCTAGATGGGGTGACCTCGATGTCAATCAGCATGTGAACAATGTTAAATATATTGGGTGGATCCTTGAG

upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g43090.1 (Oryza sativa), 3'ss of exon 6
----gtaagtcaaatgttgttgaattatgaaggttattgacatgttttatgtgtagtagtttttttt------ctattgctgatt--tttggtttctcattc--------tgatattatat---tttcaattta------cagCCTAGATGGAGTGATTTAGATGTCAATCAGCATGTTAACAATGTTAAGTACATCGGTTGGATCCTTGAG
    || ||  | |  | |||  ||  ||||  ||||    |||  | |  ||   |  ||| | |         | |  | |||  | |     ||||||         |||||||  ||    |    ||||      |||||||||||| ||||  | ||||||||||||||||| ||||||||||| || || || ||||||||||||
gtaagtcagctagacatggttacatactgaa--ttatcattatgcctcaactgctatcatttatctaagaaaaacagtaataattgatctcacccctcatttattttaaatgatatttgatggactcttgtttactgcaacagCCTAGATGGGGTGACCTCGATGTCAATCAGCATGTGAACAATGTTAAATATATTGGGTGGATCCTTGAG

upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM5G829544_T01 (Zea mays), 3'ss of exon 5
----gtaagtcaaatgt-tgttgaattatgaaggttattgacatgttttatgtgtagtagttttttttctattgctgatttttggtttctcattctgatattatattttcaatttacagCCTAGATGGAGTGATTTAGATGTCAATCAGCATGTTAACAATGTTAAGTACATCGGTTGGATCCTTGAG
    ||| | |||   |    ||  |  |    ||        |   | |     ||  || |  |   | ||||  | |     | |||||    |  | |  |||  || |   |||||||||||| ||||  | |||||||| ||||| || || || || ||||| ||||||||||||||||||
gtaagtaggacaaccatgctctgcttcctagtagtagccactgtacctgactctcag--gtatcgtgattgttgccaaatgcaaatctctcac---ggaactccatta-cattgagcagCCTAGATGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAGTATATCGGTTGGATCCTTGAG

upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G08060.2 (Glycine max), 3'ss of exon 4
gtaagtcaaatgttgttgaattatgaaggttattgacatgttttatgtgtagtagttttttttctattgctgatttttggtttctcattctgatattatattttcaatttacagCCTAGATGGAGTGATTTAGATGTCAATCAGCATGTTAACAATGTTAAGTACATCGGTTGGATCCTTGAG
||| ||||| |  | ||    | |     ||  || |||   || | | |  |    || ||||   || || ||| |  ||     ||   ||| |  || |||| ||| |||||||| ||||||||| ||||| ||||||||||||| |||||||| |||||||| || ||||| || |||
gtatgtcaactagtttt----ttttctaattgctgtcattaatt-tattttctcaaattatttcagatgttgttttctaatta---gtttacataatgcatcttcattttgcagCCTAGGTGGAGTGATCTAGATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAG

upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G21910.1 (Glycine max), 3'ss of exon 5
gtaagtcaaatgttgttgaattatgaaggttattgacatgttttatgtgtagtagttttttttctattgctgatttttggtttctcattctgatattatat-tttcaatttacagCCTAGATGGAGTGATTTAGATGTCAATCAGCATGTTAACAATGTTAAGTACATCGGTTGGATCCTTGAG
                              |||  | |  |  | |    | |  ||| |||||||      || |  | | | |  |  | ||||||| | | || |||| ||||| ||||||| |||| ||||||| |||||||||||||||||||| |||||  | || ||||| || |||
-----------------------------gtatgcaaacttcatgttatcattgatttattttctaaaat--atctcagatgttttctaatcatattatgtgtctctattttcagCCCAGATGGAATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTATGTTGGGTGGATTCTGGAG

upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G12940.2 (Glycine max), 3'ss of exon 5
gtaagtcaaatgttgttgaattatgaaggttattgacatgttttatgtgtagtagttttttttctattgctgatttttggtttctcattctgatattatattttcaat-ttacagCCTAGATGGAGTGATTTAGATGTCAATCAGCATGTTAACAATGTTAAGTACATCGGTTGGATCCTTGAG
||| ||||| |  | ||   || | |  ||| |    |  || | |   ||      || ||||   || || ||| |  ||     ||   ||  | ||| |||| | || ||| |||| ||||||||| ||||| ||||||||||||| |||||||| |||||||| |  ||||| || |||
gtatgtcaactagttttt--ttgtaattgttgtcattaatttcttttcttaaa----ttatttcagatgttgctttctaatta---gtttacattatgtatcttcattcttccagTCTAGGTGGAGTGATCTAGATATCAATCAGCATGTCAACAATGTGAAGTACATTGACTGGATTCTGGAG

upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G23560.1 (Glycine max), 3'ss of exon 5
gtaagtcaaatgttgttgaattatgaaggttattgacatgttttatgtgtagtagttttttttctattgctgatttttggtttctcattctgatattatat-tttcaatttacagCCTAGATGGAGTGATTTAGATGTCAATCAGCATGTTAACAATGTTAAGTACATCGGTTGGATCCTTGAG
                     |||| |   |  |      || | |    | |  ||| |||||||       |     ||||     |  ||| |||  | | || |||| ||||| ||||||  |||| ||||||| |||||||||||||||||||| |||||  | || ||||| || |||
--------------------gtatgcaaacttcttttcaattatgttatcattgatttattttctaaaatgtctcagatgttttctgattagatgttacgtatctctattttcagCCCAGATGGCATGATCTAGATGTGAATCAGCATGTTAACAATGTGAAGTATGTTGGGTGGATTCTGGAG

upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S167_109V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagtcaa-----atgtt-gttgaatta--tgaaggttattgacatgttttatgtgtagtagtttttt-ttctattgctgatttttggtttctcattctgatattatat--tttcaattt----acagCCTAGATGGAGTGATTTAGATGTCAATCAGCATGTTAACAATGTTAAGTACATCGGTTGGATCCTTGAG
||||||         |||| |||||| ||  |  | |||      || |   | ||||  | |  | |  ||  |      |||    | | |  ||  ||||   |  |   |||| | |     ||||| ||| | |||||||||||  | ||||||||||| ||||| || |||||||||||||||||  | |||
gtaagttgccttctgtgttcgttgaactaattctacgttgaattgatttaccacgtgtgatgggctatggtttcaaaatcaattggaaggtacgaatgttgatgagacttgacttcattgttcgtgcagCCGAGACGCAGTGATTTAGACATGAATCAGCATGTGAACAACGTGAAGTACATCGGTTGGATGATGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctattgctgatttttggtttctcattctgatattatattttcaatttacagCCTAGATGGAGTGATTTAGATGTCAATCAGCATGTTAACAATGTTAAGTACATCGGTTGGATCCTTGAG
                            ttctgat  putative branch site (score: 3)
                                       tattttc  putative PPT
                         tcattctgatattata  TA-rich tract