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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctatgaaaatattcagcagggcacaaatttgtattacatgtattttgtttcatatgctttttacataaacatcccctatattttccttacttcgggcagGTGAATATTCGTTTTCGGCGTCCTAGAAATCCTATTATTGGTGATAAATTTAGTAGCAGACATGGGCAAAAAGGTGTTTGCTCGCAGTTGTGGCCAGATA

Basic information

species Vitis vinifera
transcript Vv13s0084g00600.t01
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0084g00600.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: LOC_Os10g35290.1 (Oryza sativa), 3'ss of exon 22
--cctatgaaaatattcagcagggcacaaatttgtattacatgtattttgtttcatatgctttttacataaacatcccctatatt-ttccttacttcgggcagGTGAATATTCGTTTTCGGCGTCCTAGAAATCCTATTATTGGTGATAAATTTAGTAGCAGACATGGGCAAAAAGGTGTTTGCTCGCAGTTGTGGCCAGATA
    |     ||| || || |||       |||||   |  ||| || |  ||  | |  || | |  |   ||| |  |  | |  | | |  ||  | ||||  ||||||||| | || ||    ||||||||||| |||||||| || || || ||||||||||| ||||| || ||||| |||||||||||||| ||||
gcatttcttgaatgtt-agtaggattattgtttgtgaaa-gtgtgttctaatttgttt-tttgtcatcttggcatgcttttcactactgcatgtttttgtcagGCTAATATTCGTCTGCGTCGCGTGAGAAATCCTATAATTGGTGACAAGTTCAGCAGCAGACATGGTCAAAAGGGAGTTTGTTCGCAGTTGTGGCCTGATA

upper sequence: Vv13s0084g00600.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: GRMZM2G388892_T02 (Zea mays), 3'ss of exon 23
cctatgaaaatattcagcagggcacaaatttgtattacatgtattttgtttcatatgctttttacataaacatcccctatattttccttacttcgggcagGTGAATATTCGTTTTCGGCGTCCTAGAAATCCTATTATTGGTGATAAATTTAGTAGCAGACATGGGCAAAAAGGTGTTTGCTCGCAGTTGTGGCCAGATA
| |      |  || |  ||  |    |||| |  | |    | ||       | |  || | |  |   |||    |  | |       |||   ||||| ||| |||||| | || |||   ||||| ||||| || ||||| || || || ||  |||||||||| || ||||||||||| ||||||||||| || |
cgtgcagtgagttttaaaagtactagtatttctgatgccaacagttatgaatttgttattgtgatctcgtcatgtgtttcactacttgatctttttgcagGCGAACATTCGTCTGCGTCGTGTAAGAAACCCTATAATCGGTGACAAGTTCAGCAGTCGACATGGGCAGAAGGGTGTTTGCTCTCAGTTGTGGCCTGACA

upper sequence: Vv13s0084g00600.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: GLYMA13G26190.1 (Glycine max), 3'ss of exon 27
cctatgaaaatattcagcagggcacaaatttgta--ttacatgtattttgtttcat-atgctttttacataaacatcccctatattttccttacttcgggcagGTGAATATTCGTTTTCGGCGTCCTAGAAATCCTATTATTGGTGATAAATTTAGTAGCAGACATGGGCAAAAAGGTGTTTGCTCGCAGTTGTGGCCAGATA
   ||     || ||||  |        || ||    | |  ||  ||| ||| || |  |  |||        |     ||  || | || | || | |||||| || || |||||||| | |||  | || ||| ||||||||||||||||||| |||||||||||||| |||||||||||||| ||| ||||||||||| 
--gatttggttagtcagttgatatttttttagtgggcttctagttctttatttgattactcactttgatctgctaatttttagcttatgctca-ttggagcagGTTAACATACGTTTTCGACATCCCCGGAACCCTGTTATTGGTGATAAATTTAGCAGCAGACATGGGCAGAAAGGTGTTTGCTCTCAGCTGTGGCCAGATG

upper sequence: Vv13s0084g00600.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: GLYMA17G23500.2 (Glycine max), 3'ss of exon 1
cctatgaaaatattcagcagggcacaa---atttgtattacatgtattttgtttcatatgctttttacataaacatcccctatattttccttacttcgggcagGTGAATATTCGTTTTCGGCGTCCTAGAAATCCTATTATTGGTGATAAATTTAGTAGCAGACATGGGCAAAAAGGTGTTTGCTCGCAGTTGTGGCCAGATA
   ||     || ||||  |    |     | | |  ||| |  | |||| ||   ||| |  |||        |     |   || | |||| || | |||||| || || || ||||| | |||| | || ||| ||||||||||||||||||| || ||||||||||| ||||| |||||||| ||||||||||||||  
--gatttggttagtcagttgatatctttttactgggcttatagttctttttttgattattcactttgatctgctaatttttggcttatgctta-ttggagcagGTTAACATACGCTTTCGACATCCTCGGAACCCTGTTATTGGTGATAAATTTAGCAGTAGACATGGGCAGAAAGGCGTTTGCTCTCAGTTGTGGCCAGACG

upper sequence: Vv13s0084g00600.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: AT1G29940.1 (Arabidopsis thaliana), 3'ss of exon 24
cctatgaaaatattcagcagggcacaaatttgtattacatgtattttgttt-catatgctttttacataaacatcccctatattttccttacttcgggcagGTGAATATTCGTTTTCGGCGTCCTAGAAATCCTATTATTGGTGATAAATTTAGTAGCAGACATGGGCAAAAAGGTGTTTGCTCGCAGTTGTGGCCAGATA
                          |  ||  | | ||  |||    |   || || |   ||   | || |||      ||||||     |   |||||| |||||||||||| |||| | | ||||| || || || ||||| || || || || |||||||||||||| |||||||| || || |||||||| ||||
-----------------------gtgaggtttaactccaactatcgcatagacagattccaattggcttaaaatcta----attttcgagtttcttggcagGCGAATATTCGTTTCCGGCATGCCAGAAACCCCATAATCGGTGACAAGTTCAGCAGTAGACATGGGCAAAAGGGTGTTTGTTCTCAATTGTGGCCTGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttcatatgctttttacataaacatcccctatattttccttacttcgggcagGTGAATATTCGTTTTCGGCGTCCTAGAAATCCTATTATTGGTGATAAATTTAGTAGCAGACATGGGCAAAAAGGTGTTTGCTCGCAGTTGTGGCCAGATA
                                       tccttac  putative branch site (score: 2)
                           tcccctatattttcct  CT-rich tract
             tttttacataaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctatgaaaatattcagcagggcacaaatttgtattacatgtattttgtttcatatgctttttacataaacatcccctatattttccttacttcgggcagGTGAATATTCGTTTTCGGCGTCCTAGAAATCCTATTATTGGTGATAAATTTAGTAGCAGACATGGGCAAAAAGGTGTTTGCTCGCAGTTGTGGCCAGATA

- - -gaaaata
- - - - - - ttcagca
- - - - - - - - - - - cacaaat
- - - - - - - - - - - - - - - - - - -catgtat
- - - - - - - - - - - - - - - - - - - - - - - - - -catatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cataaac