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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatggatgaaaatggttgtcacaaacatttttgtttttaaaaaatagaaattttggcgcagttaaaactgattttgggggcatttttggtgtggtgcagCAAAATTATCGAGCTTGGATTCAATGAGAAGTTCATAAGGACATGGGAGTATTATTTTGATTATTGTGCAGCTGGTTTTAAAACTCACACTCTGGGAAAT

Basic information

species Vitis vinifera
transcript Vv05s0049g01650.t01
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01650.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 24
ttatgg-atgaaaatggttgtcacaaacatttttgtttttaaaaaatagaaattttggcgcagttaaaactgattttgggggcatttttggtgtggtgcagCAAAATTATCGAGCTTGGATTCAATGAGAAGTTCATAAGGACATGGGAGTATTATTTTGATTATTGTGCAGCTGGTTTTAAAACTCACACTCTGGGAAAT
 ||||  || ||  || |||  ||   || |||||| | | |||   |   |  |     ||     | || ||| |   |    |||| |||  |  |||  ||||| | |  || ||||||||||| || || || ||||||||||| || ||||||||||| ||||  || ||||||||  | | ||| || || |||
gtatgctattaatttgattgaaact--cacttttgtatgttaaattcaagtaactacttacaac---agctaattattatgtttatttttgtgctg-acagTGAAATTTTGGCTCTCGGATTCAATGAAAAATTTATCAGGACATGGGAATACTATTTTGATTACTGTGGTGCAGGTTTTAAGTCACTCACACTAGGGAAT

upper sequence: Vv05s0049g01650.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: GLYMA10G33310.1 (Glycine max), 3'ss of exon 24
ttatgg-atgaaaatggttgtcacaaacatttttgtttttaaaaaatagaaattttggcgcagttaaaactgattttgggggcatttttggtgtggtg-cagCAAAATTATCGAGCTTGGATTCAATGAGAAGTTCATAAGGACATGGGAGTATTATTTTGATTATTGTGCAGCTGGTTTTAAAACTCACACTCTGGGAAAT
 ||||  || ||  || |||  ||   || |||||| | | |||   | | |  |     ||     |||| ||| | |     || ||  |||| || |||  ||||||| |  || ||||| ||||| || ||||| ||||||||||| || ||||||||||| ||||  || ||||||||  ||| ||| || ||||||
gtatgttattaatttgattgaaact--cacttttgtatgttaaattcaaataactacttacaac---aactaattattgaatgtttatttttgtgctgacagTGAAATTATGGCTCTCGGATTTAATGAAAAATTCATCAGGACATGGGAATACTATTTTGATTACTGTGGTGCAGGTTTTAAGTCTCTCACACTTGGAAAT

upper sequence: Vv05s0049g01650.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: AT3G23470.1 (Arabidopsis thaliana), 3'ss of exon 13
ttatggatgaaaatggttgtcacaaacatttttgtt--tttaaaaaatagaaattttggcgcagttaaaactgattt-tgggggcatttttggtgtggtgcagCAAAATTATCGAGCTTGGATTCAATGAGAAGTTCATAAGGACATGGGAGTATTATTTTGATTATTGTGCAGCTGGTTTTAAAACTCACACTCTGGGAAAT
 ||  |||||||||     | | |||| |||    |  |||       || ||| |    |   ||  |  ||     |      |  | |  | ||  ||||  |||| ||||| ||||||||| | || || ||||||||||||||||| |||||||| || ||||||||||||||||| || ||||  || ||  |||  
gta-agatgaaaata----ttaaaaacctttcctctgttttgcttttcaggaatctgtatgttttttcatatgtccaataaaactaactattatctg-cgcagACAAATCATCGATCTTGGATTCGACGATAAATTCATAAGGACATGGGAATATTATTTCGACTATTGTGCAGCTGGTTTCAAGACTCTTACCCTTAGAAGC

upper sequence: Vv05s0049g01650.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: AT3G23510.1 (Arabidopsis thaliana), 3'ss of exon 21
ttatggatgaaaatggttgtcacaaacatttttgtttttaaaaaatagaaattttggcgcagttaaaactgattttgggggcatttttggtgtg-gtgcagCAAAATTATCGAGCTTGGATTCAATGAGAAGTTCATAAGGACATGGGAGTATTATTTTGATTATTGTGCAGCTGGTTTTAAAACTCACACTCTGGGAAAT
    | | || ||  | | |   ||||||||    | ||             |||| |    |||       || |      | | ||  | |  ||||||  |||| || |  ||||||||  |||| || ||| ||||||||||||| ||||||||||||||||| |||||||| || || ||||  ||||| ||| | 
----gtaagataaaagatatttaaaacatttcctctgtt-------------tttgtcctgtttactcacatttctatcaaaactattattatttgtgcagACAAATCATGGCTCTTGGATTTGATGATAAATTCGTAAGGACATGGGAATATTATTTTGATTATTGCGCAGCTGGATTCAAGACTCGTACTCTTGGAGAC

upper sequence: Vv05s0049g01650.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: AT3G23480.1 (Arabidopsis thaliana), 3'ss of exon 13
ttatggatgaaaatggttgtcacaaacatttttgtttt--taaaaaatagaaattttggcgcagttaaaactgattttgggggcattt-ttggtgtg-gtgcagCAAAATTATCGAGCTTGGATTCAATGAGAAGTTCATAAGGACATGGGAGTATTATTTTGATTATTGTGCAGCTGGTTTTAAAACTCACACTCTGGGAAAT
        | ||   ||  | | ||| | ||||  | |  |      |  |   ||| |     ||     |   |        | |   |  | |  | ||||  |||| || || ||||||||| | ||||| ||| ||||||||||||| |||||||| || || ||||||||||| || || ||||  || ||  |||| 
--------gtaagatgtcataataaaaacttttcctctgttgtgcttttcaggatttagtatgtttgttcatacgtccaacaaaactaactattatctgcgcagACAAATCATTGATCTTGGATTCGACGAGAAATTCTTAAGGACATGGGAATATTATTTCGACTACTGTGCAGCTGGGTTCAAGACTCTTACCCTTAGAAAC

upper sequence: Vv05s0049g01650.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: AT3G23530.1 (Arabidopsis thaliana), 3'ss of exon 21
ttatggatgaaaatggttgtcacaaacatttttgtttttaaaaaatagaaattttggcgcagttaaaactgattttgggggcatttttggtgtggtgcagCAAAATTATCGAGCTTGGATTCAATGAGAAGTTCATAAGGACATGGGAGTATTATTTTGATTATTGTGCAGCTGGTTTTAAAACTCACACTCTGGGAAAT
   |     ||||    | |   || |||||    |               |||| |  | ||| |  |  |||||      |  | |  | ||||||||  |||| || |  ||||||||  |||| || ||| ||||||| ||||| ||||||||||||||||| |||||||| || || ||||  ||||| ||||| 
--gtaagataaaaaaaatatttaaagcatttcctct--------------gtttttgttctgtttactcatattttcaacataactattat-tggtgcagACAAATCATGGCTCTTGGATTTGATGACAAATTCGTAAGGACGTGGGAATATTATTTTGATTATTGCGCAGCTGGATTCAAGACTCTTACTCTTGGAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaaattttggcgcagttaaaactgattttgggggcatttttggtgtggtgcagCAAAATTATCGAGCTTGGATTCAATGAGAAGTTCATAAGGACATGGGAGTATTATTTTGATTATTGTGCAGCTGGTTTTAAAACTCACACTCTGGGAAAT
                     aactgat  putative branch site (score: 3)
                 ttaaaactgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatggatgaaaatggttgtcacaaacatttttgtttttaaaaaatagaaattttggcgcagttaaaactgattttgggggcatttttggtgtggtgcagCAAAATTATCGAGCTTGGATTCAATGAGAAGTTCATAAGGACATGGGAGTATTATTTTGATTATTGTGCAGCTGGTTTTAAAACTCACACTCTGGGAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - atgaaaa
- - - - - - -tggttgt
- - - - - - - - - - cacaaac
- - - - - - - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - agaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttggggg