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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatacccctgactttcctaataaatttctcaactggattgattaattgggcggatattgttgcctatgcatctttagtgaagattgatttattatctgacttttgtgggctatgcagCTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTACAACATGACTTATCATCTCTGTGGGAATTAGATCTCAATGGAAAAGTTG

Basic information

species Vitis vinifera
transcript Vv12s0142g00340.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0142g00340.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G42280.2 (Glycine max), 3'ss of exon 4
gttaatacccctgactttcctaataaatttctcaactggattgattaattgggcggatattgttgcctatgcatctttagtgaagattgatttattatctgacttttgtgggctatg-cagCTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTACAACATGACTTATCATCTCTGTGGGAATTAGATCTCAATGGAAAAGTTG
|| | ||     |   ||  |  ||    |||      |||||| ||||    | ||||         |   ||  || |||| ||||| || || |||||| |||||||| | |   ||||| |||||||||||  | |||||||| ||||||||||||||| | ||||||||||||||| |||| ||| |||||||| ||||||| ||||| |||||  
gtaatta-----gttatttttggtagccctct------gattgagtaat--aactgataacaagtttaaataatgcttggtgatgattgtttcatcatctgatttttgtggaccacaacagCTCTTTCCAGATCTCAAAAAGATAGTATTCTTGGATGATGATGTAGTAGTACAACATGACATATCTTCTTTGTGGGAACTAGATCTTAATGGCAAAGTCA

upper sequence: Vv12s0142g00340.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G45720.1 (Glycine max), 3'ss of exon 2
gttaatacccctgactttcctaataaatttctcaactggattgattaattgggcggatattgttgcctatgcatctttagtgaagattgatttattatctgacttttgtgggctat-gcagCTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTACAACATGACTTATCATCTCTGTGGGAATTAGATCTCAATGGAAAAGTTG
                  |    ||||    | |    ||||  ||| |       | |    |||  |   ||  ||  |||   ||| || || |||||| |||||||| | ||  ||||| |||||||||||  ||||| |||| ||  ||||||||||| | ||||||||||||||| |||| ||| |||||||| ||||||| ||||| |||||  
----------------cgcaatttaaaaccttgagtaagatt--ttagtaataaaaacacgaatgctcagtgatgattcatga---ttgtttcataatctgatttttgtggaccatcacagCTCTTTCCAGATCTAAACAAGGTAGTATTGCTGGATGATGATGTGGTAGTACAACATGACCTATCTTCTTTGTGGGAACTAGATCTTAATGGCAAAGTCA

upper sequence: Vv12s0142g00340.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G03110.1 (Glycine max), 3'ss of exon 4
gttaatacccctgactttcctaataaatttctcaactggattgattaattgggcggatattgttgcctatgcatctttagtgaagattgatttattatctgactttt-gtgggctat-gcagCTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTACAACATGACTTATCATCTCTGTGGGAATTAGATCTCAATGGAAAAGTTG
                     | | ||   ||| | |    |  ||| |       | |    |||  |    |  | | ||| ||||| || || |||||| |||| |||| | ||  |||||||||||||||||  ||||| |||| ||  ||||||||||| ||||||||||||||||| |||| ||| | |||||| | ||||| ||||| |||||  
------------------gtaatttaaaacctcgagtaagatt-ttagtaataacaagacgaatgctaa---gtgatgattgatgattgtttcataatctgattttttgtggaccatcacagCTGTTTCCAGATCTAAACAAGGTAGTATTGCTGGATGATGATGTTGTAGTACAACATGACATATCTTCTTTATGGGAACTGGATCTTAATGGCAAAGTCA

upper sequence: Vv12s0142g00340.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G58790.1 (Arabidopsis thaliana), 3'ss of exon 4
gttaatacccctgactttcctaataaatttctcaactggattgattaattgggcggatattgttgcctatgcatctttagtgaagattgatttattatctgacttttgtgggctatgcagCTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTACAACATGACTTATCATCTCTGTGGGAATTAGATCTCAATGGAAAAGTTG
                    |||    | ||||  ||  | |  ||   || ||  | |       | ||  ||| ||        | ||   ||  |||   |||  ||| |   |||||| |||||||||||  ||||||||||||| |||||||||||| | ||||||||    ||  | || ||| | ||||||   |||||||| || |||||||
-------------------gtaaagtttctctcctctcaactc-ttctctgagcttaaaaaccattccatttatcatt--------tcga---atcttct--ttttgttggaccgcgcagCTTTTTCCAGATCTCAACAAGATAGTGTTGTTGGATGATGATGTAGTAGTACAGAGCGATCTTTCGTCTTTATGGGAAACGGATCTCAACGGTAAAGTTG

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|351032133|gb|FQ460390.1|FQ460390
EST:     GCCCCAGCTGCCTCTCCCTTATGAATCATCTACGGATTTATATTCCTGAG                         CTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTA
genomic: GCCCCAGCTGCCTCTCCCTTATGAATCATCTACGGATTTATATTCCTGAGgttaataccc ... ggctatgcagCTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTA
EST: gi|351057434|gb|FQ454116.1|FQ454116
EST:     GCCCCAGCTGCCTCTCCCTTATGAATCATCTACGGATTTATATTCCTGAG                         CTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTA
genomic: GCCCCAGCTGCCTCTCCCTTATGAATCATCTACGGATTTATATTCCTGAGgttaataccc ... ggctatgcagCTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTA
EST: gi|351045925|gb|FQ441308.1|FQ441308
EST:     GCCCCAGCTGCCTCTCCCTTATGAATCATCTACGGATTTATATTCCTGAG                         CTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTA
genomic: GCCCCAGCTGCCTCTCCCTTATGAATCATCTACGGATTTATATTCCTGAGgttaataccc ... ggctatgcagCTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTA
EST: gi|351022143|gb|FQ438728.1|FQ438728
EST:     GCCCCAGCTGCCTCTCCCTTATGAATCATCTACGGATTTATATTCCTGAG                         CTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTA
genomic: GCCCCAGCTGCCTCTCCCTTATGAATCATCTACGGATTTATATTCCTGAGgttaataccc ... ggctatgcagCTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTA
EST: gi|352790288|gb|FQ481487.1|FQ481487
EST:     GCCCCAGCTGCCTCTCCCTTATGAATCATCTACGGATTTATATTCCTGAG                         CTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTA
genomic: GCCCCAGCTGCCTCTCCCTTATGAATCATCTACGGATTTATATTCCTGAGgttaataccc ... ggctatgcagCTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTA
EST: gi|352790808|gb|FQ478531.1|FQ478531
EST:     GCCCCAGCTGCCTCTCCCTTATGAATCATCTACGGATTTATATTCCTGAG                         CTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTA
genomic: GCCCCAGCTGCCTCTCCCTTATGAATCATCTACGGATTTATATTCCTGAGgttaataccc ... ggctatgcagCTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctatgcatctttagtgaagattgatttattatctgacttttgtgggctatgcagCTGTTTCCAGATCTTGACAAGATAGTGTTCTTGGATGATGATATTGTAGTACAACATGACTTATCATCTCTGTGGGAATTAGATCTCAATGGAAAAGTTG
                               atctgac  putative branch site (score: 3)
                 aagattgatttattat  TA-rich tract