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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtatggtctttgtgcatgcccggatcatttgttggatgagtggaaggttaaggatgaaaaaaggtagctaataatgcttttagttccccaattttcagGATATCAAGGCATTATTTCCTTCTGATTGCAATCCATTCTATGCTGGTTTTGGAAACCGGGACACTGATGAGTTTAGCTACCTTAAGGTTGGAATTCCAA

Basic information

species Vitis vinifera
transcript Vv18s0001g10680.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os11g40080.1 (Oryza sativa), 3'ss of exon 7
---------gtgtatggtctttgtgcatgcccggatcatttgttggatgagtggaaggttaaggatgaa---aaaaggtagctaataatgc-ttttagttccccaatttt---cagGATATCAAGGCATTATTTCCTTCTGATTGCAATCCATTCTATGCTGGTTTTGGAAACCGGGACACTGATGAGTTTAGCTACCTTAAGGTTGGAATTCCAA
           | |         |  ||    | | |||   ||| || | ||   | |      ||     |  |  ||  |  ||     | ||  ||| ||  |||    |||| |||||| ||| |||||||| |||| |  ||||||||||||||||| ||||||||  | || || |||||| |||| ||||| |||||||| ||||| |
gtcagtactcagcaacacaaagataaatatatgaa-catacattgaataattgcttgctcttcattgcgctcatgaaataattcgtaccaagtcttgattcacctgtttcacacagGCTATCAAAGCACTATTTCCTCCTGACTCAAATCCATTCTATGCTGGATTTGGAAATAGAGATACAGATGAGCTTAGTTACCTCAAGGTTGGGATTCCTA

upper sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA06G04230.1 (Glycine max), 3'ss of exon 14
gtgtatggtctttgtgcatgcccggatcatttgttggatgagtggaaggttaaggatgaaaaaaggtagctaataatgcttttagttccccaattttcagGATATCAAGGCATTATTTCCTTCTGATTGCAATCCATTCTATGCTGGTTTTGGAAACCGGGACACTGATGAGTTTAGCTACCTTAAGGTTGGAATTCCAA
             ||   |  || | |  |   |   || |   | |  |||  |     | || ||   |||      ||| | ||      |  |||||| ||||||||| | |||||||||||| ||| ||||||||||||||||||||| ||  |||| ||||||||  | |||||||||||||||||||||||  
-------------gttagtttcccgctgctacatattataatgagcatattacagtc---ataatgttattaaagtcaatttgaatttttatgtcatcagGACATCAAGGCACTTTTTCCTTCTGATAGCAGTCCATTCTATGCTGGTTTTGGTAATAGGGATACTGATGAAATCAGCTACCTTAAGGTTGGAATTCCCC

upper sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA04G04060.1 (Glycine max), 3'ss of exon 13
gtgtatggtctttgtgcatgcccggatcatttgttggatgagtggaaggttaaggatgaaaaaaggtagctaataatgcttttagttccccaattttcagGATATCAAGGCATTATTTCCTTCTGATTGCAATCCATTCTATGCTGGTTTTGGAAACCGGGACACTGATGAGTTTAGCTACCTTAAGGTTGGAATTCCAA
             ||   |  || | |  |   |   |  |     |  |||        | || ||   |||      ||| | ||      |  |||||| ||||||||| | |||||||||||| ||| ||||||||||||||||||||| ||  |||| || |||||  | |||||||||||||||||||||||  
-------------gttagtttcccgctgctacatattacaatgatcatattacattc---ataatgttattaaagtctatttgaatttttatgtcatcagGACATCAAGGCACTTTTTCCTTCTGATAGCAGTCCATTCTATGCTGGTTTTGGTAATAGGGATACGGATGAAATCAGCTACCTTAAGGTTGGAATTCCCC

upper sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA17G36130.1 (Glycine max), 3'ss of exon 9
gtgtatggtctttgtgcatgcccggatcatttgttggatgagtggaaggttaagga-tgaaaaaaggtagctaataatgcttttagttccccaattttcagGATATCAAGGCATTATTTCCTTCTGATTGCAATCCATTCTATGCTGGTTTTGGAAACCGGGACACTGATGAGTTTAGCTACCTTAAGGTTGGAATTCCAA
           ||  |    | |  | |     |||    | |  |   ||    | |      |  |   |||  ||   |  | ||       || ||||| || |||||| | |||||| | ||||| ||||| ||||||||||||||||||||  |||| || |||||  | || ||||||||||||||||| ||||
----------gttaggttcccactaaactaaaattgacaaaatttatttttttccactatggtcatattattaaacataagtggaattttaatgcttccagGACATTAAGGCACTTTTTCCTCCAGATTGGAATCCGTTCTATGCTGGTTTTGGAAATAGGGATACCGATGAAGTCAGTTACCTTAAGGTTGGAATCCCAA

upper sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G42870.2 (Arabidopsis thaliana), 3'ss of exon 8
gtgtatggtctttgtgcatgcccggatcatttgttggatgagtggaaggttaaggatgaaaaaaggtagctaataatgcttttagttccccaattttcagGATATCAAGGCATTATTTCCTTCTGATTGCAATCCATTCTATGCTGGTTTTGGAAACCGGGACACTGATGAGTTTAGCTACCTTAAGGTTGGAATTCCAA
           ||     |   ||| |  |||  ||  ||  || |   | | |       ||       |||    | ||||    ||  ||| | ||||| ||   ||  || |||||| | ||   ||| |||||||||||||||||||||||| | ||||| |||||| | ||||||||||| || ||||| ||  
----------gttagttttatgcgggtttttttatgtctgt-tgaactctcatgtcctctgaactacgtttaactcggttttt----ccaaaatatacagGAGATACGGGGCTTGTTTCCTCCCGAACACAACCCATTCTATGCTGGTTTTGGAAACAGAGACACAGATGAGATAAGCTACCTTAAAGTCGGAATCCCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggttaaggatgaaaaaaggtagctaataatgcttttagttccccaattttcagGATATCAAGGCATTATTTCCTTCTGATTGCAATCCATTCTATGCTGGTTTTGGAAACCGGGACACTGATGAGTTTAGCTACCTTAAGGTTGGAATTCCAA
                      agctaat  putative branch site (score: 3)
                                        ttcccc  putative PPT
                         taataatgctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtatggtctttgtgcatgcccggatcatttgttggatgagtggaaggttaaggatgaaaaaaggtagctaataatgcttttagttccccaattttcagGATATCAAGGCATTATTTCCTTCTGATTGCAATCCATTCTATGCTGGTTTTGGAAACCGGGACACTGATGAGTTTAGCTACCTTAAGGTTGGAATTCCAA

-tgtatgg
- - - - - - - - catgccc
- - - - - - - - - - - - - - - ttgttgg
- - - - - - - - - - - - - - - - - - - tgagtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agttccc