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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggggtttaatcatactggggtttaagaatgtcattcttcctataaagttaaatgttatttccccacaactgaggatatttgatttttcatttttccttagTTCATATCGATCCCGGATGAAAGGTACGATGAGTATAGAAGAAGCTCAGATTTTATAAAGGAATACATTTTCCCTGGTGGATGCTTGCCTTCATTAAGTA

Basic information

species Vitis vinifera
transcript Vv05s0049g01620.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01620.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os12g16650.2 (Oryza sativa), 3'ss of exon 20
ggggtttaatcatactggggtttaagaatgtcattcttcctataaagttaaatgttatttccccacaactgaggatatttgatttttcatttttccttagTTCATATCGATCCCGGATGAAAGGTACGATGAGTATAGAAGAAGCTCAGATTTTATAAAGGAATACATTTTCCCTGGTGGATGCTTGCCTTCATTAAGTA
   || |   || ||     |||   | |||||||         |   | | ||||  |    | ||  | |   ||  ||       ||| ||||  |||| || || || ||||| ||| |||| ||||||||  | ||||||||||| ||||| || |||||||| ||||||||||||||| | |||||  | | | 
---gtgtgtacaaac-aacctttgtcattgtcatt--------gacactgactgttgatatatcccacttaaatttacatggg-----attattcc--agTTTATCTCAATTCCGGAGGAACGGTATGATGAGTACCGGAGAAGCTCAGACTTTATTAAAGAATACATATTCCCTGGTGGATGCCTTCCTTCTCTGACTC

upper sequence: Vv05s0049g01620.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT3G23530.1 (Arabidopsis thaliana), 3'ss of exon 19
ggggtttaatcatactggggtttaagaatgtcattcttcctataaagttaaatgttatttcccca-caactgaggatattt--gatttttcatttttccttagTTCATATCGATCCCGGATGAAAGGTACGATGAGTATAGAAGAAGCTCAGATTTTATAAAGGAATACATTTTCCCTGGTGGATGCTTGCCTTCATTAAGTA
         | ||| |   | |      | |   |||||| | | | |   |    |||||   | ||  ||||  | |||  ||| |||    | |    ||||||||||||| || || ||  | ||| ||||||| |||  ||| |||||||| || || |||||||| ||||||||||||||| | ||||| |||   |
--------gtaata-tatagctcttccttatttctcttccgagacattatcaaaacatttcataatcatttgagcctttttatgatgttttgactgtaac-agTTCATATCGATACCCGAAGAGCGTTACAATGAGTACAGACTAAGTTCAGATTTCATTAAAGAATACATATTCCCTGGTGGATGCCTTCCTTCTTTAGCCA


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttaaatgttatttccccacaactgaggatatttgatttttcatttttccttagTTCATATCGATCCCGGATGAAAGGTACGATGAGTATAGAAGAAGCTCAGATTTTATAAAGGAATACATTTTCCCTGGTGGATGCTTGCCTTCATTAAGTA
                               atttgat  putative branch site (score: 5)
                                tttgatttttcatttt  CT-rich tract
                             atatttgatttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggggtttaatcatactggggtttaagaatgtcattcttcctataaagttaaatgttatttccccacaactgaggatatttgatttttcatttttccttagTTCATATCGATCCCGGATGAAAGGTACGATGAGTATAGAAGAAGCTCAGATTTTATAAAGGAATACATTTTCCCTGGTGGATGCTTGCCTTCATTAAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
ggggttt
- - - - - - - - - - - - -gaatgtc
- - - - - - - - - - - - - - - - -ttcttcc