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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgaaccttcttcagctacaccaagttaaaaaagtgtcatagttttaagcttaagagagatgaaaggcaccattgtgcttacgttcttcttcagtttttttttgttatccccatgttttgggagaaagagggctctgtcattggacatatttatctaatatgaaccacaattgctcttgttgaagGTCTATGGTGAATTGCATCACGCTGAATTCAACAAGCAGAGTAGTTCTTGCTAGCTGTCGTAATGCTTTTACAATG

Basic information

species Vitis vinifera
transcript Vv13s0156g00080.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0156g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G16870.4 (Glycine max), 3'ss of exon 1
gtaatgaaccttcttcagctacaccaagttaaaaaagtgtcatagttttaagcttaagagagatgaaaggcaccattgtgcttacgttcttcttcagtttttttttgttatccccatgttttgggagaaagagggctct--gtcattggacata--tttatct-----aatatgaaccacaattgctcttgttgaagGTCTATGGTGAATTGCATCACGCTGAATTCAACAAGCAGAGTAGTTCTTGCTAGCTGTCGTAATGCTTTTACAATG
                                                                                                  |       || | | |     | ||  | | | | || ||   | | ||  |  ||  ||||| |     | | |   |    ||||||||| ||||||||| ||||||| ||||||||||||||| || ||||||||||| |  || ||||||||||| ||||||||||| |||
------------------------------------------------------------------------------------------------agtaacaccagtgaactctgcaatctgacaaagaaaaggttcctagcccttcaatttaactttatgttcatcagtgtcttctttgattgctctt-ttgaagGTCCATGGTGAGTTGCATCACGCTGAACTCTACAAGCAGAGTGGCACTGGCTAGCTGTCGCAATGCTTTTACCATG

upper sequence: Vv13s0156g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G42210.1 (Glycine max), 3'ss of exon 4
gtaatgaaccttcttcagctacaccaagttaaaaaagtgtcatagttttaagcttaagagagatgaaaggcaccattgtgcttacgttcttcttcagtttttttttgttatccccatgttttgggagaaagag---ggctctgtcattggac---atatttatctaatatgaaccacaattgctcttgttgaagGTCTATGGTGAATTGCATCACGCTGAATTCAACAAGCAGAGTAGTTCTTGCTAGCTGTCGTAATGCTTTTACAATG
                                                                                            | ||    |       ||     ||| |   | | || |       | ||    ||  ||   || || || || | |   |    ||||||||| ||||||||| ||||||| ||||||||| ||||| || ||||||||||| |  || ||||||||||| ||||||||||| |||
--------------------------------------------------------------------------------------------tacatgcatagaagaataataaaatgataaagaaaaaggttcctaacccttcagtttaactttatgttcat-tagtgtctgctttgattgctctt-ttgaagGTCCATGGTGAGTTGCATCACACTGAACTCTACAAGCAGAGTGGCACTGGCTAGCTGTCGCAATGCTTTTACCATG

upper sequence: Vv13s0156g00080.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G44280.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatgaaccttcttcagctacaccaagttaaaaaagtgtcatagttttaagcttaagagagatgaaaggcaccattgtgcttacgttcttcttcagtttttttttgttatccccatgttttgggagaaagagggctctgtcattggacatatttatctaatatgaaccacaattgctcttgttgaagGTCTATGGTGAATTGCATCACGCTGAATTCAACAAGCAGAGTAGTTCTTGCTAGCTGTCGTAATGCTTTTACAATG
                                                                             ||       |  ||||||  |||  |||  |  ||||  |   ||      ||    | |   ||| ||   || || || |  | || |  |   ||    |  ||  ||| ||||||| |||||||| ||  |||||||||||||||||||||  ||  | ||||  |||||||| ||||  |||
-----------------------------------------------------------------------------gtaaaacaatctttcttc--tttcatttgatcttccctttagattaatctcaaa---gtttaatcagtgag-atgttcattt--tttgcataatctttatgttcttt--agGGCTATGGTTAATTGCATTACATTGAATTCAACAAGCAGAGTAGCACTAACAAGCTCCCGTAATGCGTTTAGCATG

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|161706475|gb|FC054996.1|FC054996
EST:     TTTGCCGCAATCTTCAATGTGGGCTGGGCTGCTACTCAAGTTTCACACAT                         GTCTATGGTGAATTGCATCACGCTGAATTCAACAAGCAGAGTAGTTCTTGC
genomic: TTTGCCGCAATCTTCAATGTGGGCTGGGCTGCTACTCAAGTTTCACACATgtaatgaacc ... cttgttgaagGTCTATGGTGAATTGCATCACGCTGAATTCAACAAGCAGAGTAGTTCTTGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctctgtcattggacatatttatctaatatgaaccacaattgctcttgttgaagGTCTATGGTGAATTGCATCACGCTGAATTCAACAAGCAGAGTAGTTCTTGCTAGCTGTCGTAATGCTTTTACAATG
                      atctaat  putative branch site (score: 3)
                                        ttgctctt  putative PPT
                atatttatctaatatg  TA-rich tract