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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgccagaggattaaaaatatagtagtgttctttgtcttttgctctgttgttaatattgatttgaaggaaattttatacaattttctctctatttgcagCTGACGAGGGCTTACTTTGCATTCTTGGAGGTTTTATTCAACAGCCATATTGTTTTTATATTGAATCTGGATACAAACACCTTTATGCATATAGTTGGTT

Basic information

species Vitis vinifera
transcript Vv13s0067g01920.t01
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g01920.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA06G00520.1 (Glycine max), 3'ss of exon 17
---catgccagaggattaaaaatatagtagtgttctttgtcttttgctctgttgttaatattgatttgaaggaaattttatacaattttctctctatttgcagCTGACGAGGGCTTACTTTGCATTCTTGGAGGTTTTATTCAACAGCCATATTGTTTTTATATTGAATCTGGATACAAACACCTTTATGCATATAGTTGGTT
     |   |      |    |  ||   ||    || || || ||     |||  ||   |   || |    ||| | |   | ||||  || | | ||||||| || |||||||| ||||| |||||||||||||| ||||||||||| ||   |||| |||| ||  |||| |||||||||||||||||||| ||||| |
atcttttttatcttgctcctgaattatgtgttgggttagttttctgtcagcttgcgaaa--tacattaagatgaatctcacttagtttttgcttt-tatgcagCTAACAAGGGCTTATTTTGCCTTCTTGGAGGTTTTGTTCAACAGCCACATCACTTTTGTATTAAACTTGGACACAAACACCTTTATGCATATGGTTGGCT

upper sequence: Vv13s0067g01920.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA04G00430.1 (Glycine max), 3'ss of exon 23
---catgccagaggattaaaaatatagtagtgttctttgtcttttgctctgttgttaatattgatttgaaggaaattttatacaattttctctctatttgcagCTGACGAGGGCTTACTTTGCATTCTTGGAGGTTTTATTCAACAGCCATATTGTTTTTATATTGAATCTGGATACAAACACCTTTATGCATATAGTTGGTT
     |   |    | |    |  ||    |    || || || ||     |||  ||   |   || | |  ||| | |   | ||||  || | | ||||| | || |||||||| ||||| |||||||| ||||| ||||||||||| ||   |||| |||| ||  |||| |||||||||||||||||||| ||||| |
tccttttttatcttactcctgaattatgtattggattagttttctgtcagtttgccaaa--tacattaaggtgaatctcacttagtttttgcttt-tatgcagTTAACAAGGGCTTATTTTGCCTTCTTGGAAGTTTTGTTCAACAGCCACATCACTTTTGTATTAAACTTGGACACAAACACCTTTATGCATATGGTTGGCT
















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|161712964|gb|FC062090.1|FC062090
EST:     TAAAGATGACACTCTCAATTCCTTTGGCTGATATATTGGCTTTTCGGAAG                         CTGACCAGGGCTTACTTTGCATTCTTGGAGGTTTTATTCAACAGCCATATT
genomic: TAAAGATGACACTCTCAATTCCTTTGGCTGATATATTGGCTTTTCGGAAGgtatgtagga ... ctatttgcagCTGACGAGGGCTTACTTTGCATTCTTGGAGGTTTTATTCAACAGCCATATT
EST: gi|351036060|gb|FQ463905.1|FQ463905
EST:     TAAAGATGACACTCTCAATTCCTTTGGCTGATATATTGGCTTTTCGGAAG                         CTGACGAGGGCTTACTTTGCATTCTTGGAGGTTTTATTCAACAGCCATATT
genomic: TAAAGATGACACTCTCAATTCCTTTGGCTGATATATTGGCTTTTCGGAAGgtatgtagga ... ctatttgcagCTGACGAGGGCTTACTTTGCATTCTTGGAGGTTTTATTCAACAGCCATATT
EST: gi|351026572|gb|FQ432470.1|FQ432470
EST:     TAAAGATGACACTCTCAATTCCTTTGGCTGATATATTGGCTTTTCGGAAG                         CTGACGAGGGCTTACTTTGCATTCTTGGAGGTTTTATTCAACAGCCATATT
genomic: TAAAGATGACACTCTCAATTCCTTTGGCTGATATATTGGCTTTTCGGAAGgtatgtagga ... ctatttgcagCTGACGAGGGCTTACTTTGCATTCTTGGAGGTTTTATTCAACAGCCATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttgttaatattgatttgaaggaaattttatacaattttctctctatttgcagCTGACGAGGGCTTACTTTGCATTCTTGGAGGTTTTATTCAACAGCCATATTGTTTTTATATTGAATCTGGATACAAACACCTTTATGCATATAGTTGGTT
          tattgat  putative branch site (score: 3)
                                     ttttctctctatttgc  putative PPT
      ttaatattgatttgaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgccagaggattaaaaatatagtagtgttctttgtcttttgctctgttgttaatattgatttgaaggaaattttatacaattttctctctatttgcagCTGACGAGGGCTTACTTTGCATTCTTGGAGGTTTTATTCAACAGCCATATTGTTTTTATATTGAATCTGGATACAAACACCTTTATGCATATAGTTGGTT

catgcca
- - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - -cttttgc
- - - - - - - - - - - - - - - - - - - - - - -ctgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaggaaa