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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaagatagaaaagaatcttcttttttgtggacgtgcagtttgtactaaactgatttaggcatttaggctctgatgcaatgttatttgtcattcttgcagTTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCATATCTCAACACTTATGATGGGCGAACCATCCGCTACCCTGATCCTCTGA

Basic information

species Vitis vinifera
transcript Vv06s0004g07150.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g07150.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G31270.1 (Glycine max), 3'ss of exon 4
----tcaagatagaaaagaatcttcttttttgtggacgtgcagtttgtactaaactg-atttaggcatttaggctctgatgcaatgttatttgtcattcttgcagTTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCATATCTCAACACTTATGATGGGCGAACCATCCGCTACCCTGATCCTCTGA
    |  || |  | ||     ||  ||||  ||||  |    ||  |  |   ||| |  |   | ||   |   |  | |  |  | |||| | || ||  |||||||||||||||||||  | ||||| || ||||| || ||||| ||||| ||| | ||||| || |||||||| ||||||||||| ||||| || || |
gcttttgagctctataaa----tttgttttgctggatcttattttaatgtttttctgtagattttctttctagtgattttactctaatttttgcc-ttgttatagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGTATCCCCTATTTAAACACATACGATGGGCGCACCATCCGCTATCCTGACCCACTAA

upper sequence: Vv06s0004g07150.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G06440.1 (Glycine max), 3'ss of exon 4
----tcaagatagaaaagaatcttcttttttgtggacgtgcagtttgtactaaactgatttaggcatttaggctctgatgcaatgttatttgtcattcttgcagTTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCATATCTCAACACTTATGATGGGCGAACCATCCGCTACCCTGATCCTCTGA
    |  ||    | ||   | || | || | |     | || | | |  |     |||||      |   | | | |  |  |  | |||| | || || ||||||||||||||||||||  | ||||| || ||||| || ||||| ||||| ||| | ||||| ||||| || || ||||||||||| ||||| || || |
gcttttgagcactataaatttgttttgttgtatcttatttcaatgttt-ttctgtagattttctttctagtgatttcactc--taatttttgcc-ttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCCTATTTGAACACATATGACGGCCGTACCATCCGCTATCCTGACCCACTAA
















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|110702679|gb|EE078871.1|EE078871
EST:     ACACCAAGGGCCGGTTTCGTCTCCACTCAATTAGGGATGAAGAGGCTAAG                         TTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCA
genomic: ACACCAAGGGCCGGTTTCGTCTCCACTCAATTAGGGATGAAGAGGCTAAGgtaggtgttt ... attcttgcagTTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCA
EST: gi|30296893|gb|CB973687.1|CB973687
EST:     ACACCAAGGGCCGGTTTCGTCTCCACTCAATTAGGGATGAAGAGGCTAAG                         TTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCA
genomic: ACACCAAGGGCCGGTTTCGTCTCCACTCAATTAGGGATGAAGAGGCTAAGgtaggtgttt ... attcttgcagTTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCA
EST: gi|110701173|gb|EE078481.1|EE078481
EST:     ACACCAAGGGCCGGTTTCGTCTCCACTCAATTAGGGATGAAGAGGCTAAG                         TTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCA
genomic: ACACCAAGGGCCGGTTTCGTCTCCACTCAATTAGGGATGAAGAGGCTAAGgtaggtgttt ... attcttgcagTTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCA
EST: gi|33406463|gb|CF212090.1|CF212090
EST:     ACACCAAGGGCCGGTTTCGTCTCCACTCAATTAGGGATGAAGAGGCTAAG                         TTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCA
genomic: ACACCAAGGGCCGGTTTCGTCTCCACTCAATTAGGGATGAAGAGGCTAAGgtaggtgttt ... attcttgcagTTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCA
EST: gi|110688373|gb|EE066853.1|EE066853
EST:     ACACCAAGGGCCGGTTTCGTCTCCACTCAATTAGGGATGAAGAGGCTAAG                         TTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCA
genomic: ACACCAAGGGCCGGTTTCGTCTCCACTCAATTAGGGATGAAGAGGCTAAGgtaggtgttt ... attcttgcagTTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCA
EST: gi|110700067|gb|EE077679.1|EE077679
EST:     ACACCAAGGGCCGGTTTCGTCTCCACTCAATTAGGGATGAAGAGGCTAAG                         TTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCA
genomic: ACACCAAGGGCCGGTTTCGTCTCCACTCAATTAGGGATGAAGAGGCTAAGgtaggtgttt ... attcttgcagTTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaactgatttaggcatttaggctctgatgcaatgttatttgtcattcttgcagTTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCATATCTCAACACTTATGATGGGCGAACCATCCGCTACCCTGATCCTCTGA
                                           tcattctt  CT-rich tract
                                aatgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaagatagaaaagaatcttcttttttgtggacgtgcagtttgtactaaactgatttaggcatttaggctctgatgcaatgttatttgtcattcttgcagTTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCATATCTCAACACTTATGATGGGCGAACCATCCGCTACCCTGATCCTCTGA

- - - - -aaaagaa
- - - - - - - - - - - - -ttgtgga
- - - - - - - - - - - - - - - - - tgcagtt
- - - - - - - - - - - - - - - - - - - - - - - -aaactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgcaa