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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaatcttgcatggattgaatttctttggggaagaaaatcacatatgacatatgcacatatctgattcgcctttttgcaaattctgttttgcagAACAAATGCAATGTGGGCTATGCTTTTGTCAACATGATTGATCCTCTTCATATTGTTCCATTCCATCAG

Basic information

species Vitis vinifera
transcript Vv17s0000g00240.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 12
gtaagtaaatcttgcatggattgaatttctttggggaagaaaatcacatatgacatatgcacatatctgattcgcctttttgcaaattc-tgttttgcagAACAAATGCAATGTGGGCTATGCTTTTGTCAACATGATTGATCCTCTTCATATTGTTCCATTCCATCAG
             |  |   ||   |||||| | | || || ||  ||  ||  |  | || || || |    | |||||   |  |||   |||  ||||||||||| |||||||| ||||||||| |||| |||| |||||| |  || ||  | |||||| || ||
-------------gtctactttttttttcttagtgtaa-aagattgcaactgtga-gtaca-atttcaggactgacttttgcaatgttcacttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G01040.1 (Glycine max), 3'ss of exon 12
gtaagtaaatcttgcatggattgaatttctttggggaagaaaatcacatatgacatatgcacatatctgattcgcctttttgcaaattctgttttgcagAACAAATGCAATGTGGGCTATGCTTTTGTCAACATGATTGATCCTCTTCATATTGTTCCATTCCATCAG
|||||||  ||| |      |    |||| ||  |  |  |||||| | ||         |  | ||| |||    | |      |||       |||||||||||| ||||| |||||||| ||  | |||||||||||||||  ||| ||| |||| |||||||||
gtaagtatttctggttgatttattctttccttttgagaagaaatcataaat---------atgtttctaattttagtctacaacgatt-------gcagAACAAATGTAATGTTGGCTATGCATTCATAAACATGATTGATCCTGGTCAAATTATTCCTTTCCATCAG

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA06G17250.1 (Glycine max), 3'ss of exon 10
--gtaagtaaatc--ttgcatggattgaatttctttggggaagaaaatcacata---------tgacatatgcacatatctgattcgcctttttgcaaattctgt-----tttgcagAACAAATGCAATGTGGGCTATGCTTTTGTCAACATGATTGATCCTCTTCATATTGTTCCATTCCATCAG
   |  |  |||   || || ||   | |||| |||||    |  | |  | |          | | ||      ||     ||  |  | |  |  ||||||        |||||||||||||| ||||| |||||||| ||  |||| ||||||||||||   || ||| |||||||||| |||
gtatttgccaattgatttcaaggcaagtatttatttggacttgctagttgcttgattctttacttaaatgaagcaattataaatgtgtttctaagGCAATTCTACAAATGGTTGCAGAACAAATGTAATGTTGGCTATGCATTCATCAATATGATTGATCCTGGACAAATTATTCCATTCCACCAG

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 11
----gtaag-----taaatcttgcatggattgaatttctttggggaagaaaatcaca---tatgacatatgcacatatctgattcgcctttttgcaaattctgttttgcagAACAAATGCAATGTGGGCTATGCTTTTGTCAACATGATTGATCCTCTTCATATTGTTCCATTCCATCAG
    | | |     ||  | ||  ||  |   || |  | |   | ||| |   | |   | ||  || |    ||| |    |   ||  |   |   | |  ||| |||||||||||||||||||| ||||||||  ||||  | ||||| |||    | ||||| |||||   | ||
gcaagcaggcgtcctaccttttttatataagaaagtcttattaagcagacacgtagaggttttggtattttgcaataacgatctaatctaatcttaccctgtcattt-cagAACAAATGCAATGTGGGATATGCTTTCATCAATCTTATTGAACCTGAAAAGATTGTCCCATTTTTTAAG

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|33404602|gb|CF210229.1|CF210229
EST:     AACATCATCGAGGAACTTATGATTTTATTTATTTGCCAATTGACTTCAAA                         AACAAATGCAATGTGGGCTATGCTTTTGTCAACATGATTGATCCTCTTCAT
genomic: AACATCATCGAGGAACTTATGATTTTATTTATTTGCCAATTGACTTCAAAgtaagtaaat ... tgttttgcagAACAAATGCAATGTGGGCTATGCTTTTGTCAACATGATTGATCCTCTTCAT
EST: gi|110376881|gb|EC941957.1|EC941957
EST:     AACATCATCGAGGAACTTATGATTTTATTTATTTGCCAATTGACTTCAAA                         AACAAATGCAATGTGGGCTATGCTTTTGTCAACATGATTGATCCTCTTCAT
genomic: AACATCATCGAGGAACTTATGATTTTATTTATTTGCCAATTGACTTCAAAgtaagtaaat ... tgttttgcagAACAAATGCAATGTGGGCTATGCTTTTGTCAACATGATTGATCCTCTTCAT
EST: gi|161716528|gb|FC065225.1|FC065225
EST:     AACATCATCGAGGAACTTATGATTTTATTTATTTGCCAATTGACTTCAAA                         AACAAATGCAATGTGGGCTATGCTTTTGTCAACATGATTGATCCTCTTCAT
genomic: AACATCATCGAGGAACTTATGATTTTATTTATTTGCCAATTGACTTCAAAgtaagtaaat ... tgttttgcagAACAAATGCAATGTGGGCTATGCTTTTGTCAACATGATTGATCCTCTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatatgacatatgcacatatctgattcgcctttttgcaaattctgttttgcagAACAAATGCAATGTGGGCTATGCTTTTGTCAACATGATTGATCCTCTTCATATTGTTCCATTCCATCAG
                    atctgat  putative branch site (score: 4)
                                          ttctgtttt  putative PPT
                                       aaattct  TA-rich tract