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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaatgattgtatgcaggctctcaccttctgtttaaattttggacatattacacactgattttgacgtgttacttagatctttgcactattctatttcagGGCTTAAAGACCTTTCTGATTTTCTTCCTGCTTCTTTGGCAACCATTGCAAGTTACTTTTCTGCTGAAGTAACACGCGGTATTTGGAAACCAGCTTTTAT

Basic information

species Vitis vinifera
transcript Vv07s0104g00390.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0104g00390.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os07g11000.1 (Oryza sativa), 3'ss of exon 10
------------------------------------------------gaaatgattgtatgcaggctctcac--cttctgtttaaattttgg-acatattacacactgattttgacgtgttacttagatctttgcacta----ttctatttcagGGCTTAAAGACCTTTCTGATTTTCTTCCTGCTTCTTTGGCAACCATTGCAAGTTACTTTTCTGCTGAAGTAACACGCGGTATTTGGAAACCAGCTTTTAT
                                                   ||  |||| || |   |   |    |   |  | ||  ||   |  ||      |||   ||  | ||| |  | ||   ||   ||||    ||| ||| |||| || ||||| ||  |||||||||| ||||| ||| | || || || | |||||||||||| || ||||||||||| ||| |||||||||| || || ||
gtttgtttttgccgattctttttttttttttttgacgtaaaatttttgccgattcttgtttgaaaattaagatgattgaagagtgaaccttattatttaaccattactatgttctatgtgatcatcagtgtttgatactaccttttccattccagGTCTCAAAGATCTGACTGATTTTCTCCCTGCATCTCTTGCGACAATAGTAAGTTACTTTTCAGCCGAAGTAACACGAGGTGTTTGGAAACCGGCATTCAT

upper sequence: Vv07s0104g00390.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA03G30760.1 (Glycine max), 3'ss of exon 13
---gaaatgattgtatgcaggctctcaccttctgtttaaattttggacatattacacactgattttgacgtgttacttagatctttgcactattctatttcagGGCTTAAAGACCTTTCTGATTTTCTTCCTGCTTCTTTGGCAACCATTGCAAGTTACTTTTCTGCTGAAGTAACACGCGGTATTTGGAAACCAGCTTTTAT
      ||  |  ||   |   |  || |||   ||   |   |        |  |   ||||||| ||||  |  ||   | |||    | |||| | ||||| || ||||| ||  | ||||||||||| ||||||||||  ||||||||||| |||||||| |||||||| ||||| || || ||||| ||| |||||||
ggttgtattgtaatactgatttttccaactttgtttggtacgcttcttgctgtgtaatttgattttcacgttctttttttgttttt---tttttctttctcagGTCTCAAAGATCTAGCCGATTTTCTTCCAGCTTCTTTGGTTACCATTGCAAGCTACTTTTCAGCTGAAGTTACACGGGGCATATGGAAGCCATCTTTTAT

upper sequence: Vv07s0104g00390.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA05G09220.1 (Glycine max), 3'ss of exon 11
----------gaaatgattgtatgcaggctctcaccttctgtttaaattttggacatattacacactgattttgacgtgttacttagatctttgcactattctatttcagGGCTTAAAGACCTTTCTGATTTTCTTCCTGCTTCTTTGGCAACCATTGCAAGTTACTTTTCTGCTGAAGTAACACGCGGTATTTGGAAACCAGCTTTTAT
          ||| | |||  |    || |  ||   |||   |||  |||  || | |   |  ||| ||        |||   || | | |||   ||| ||| | ||| || ||||| ||| ||||||||||||| ||  ||||||  ||||||| ||| ||||| ||  ||||||||||||| || || ||||| || ||||||||
gtatgtttgggaattcattaaac-tgggttgccaatgtct---taacctttaaacttttctaaggctgtttgc------ttaggaagttatctgcttgattttatcttagGTCTCAAAGATCTTGCTGATTTTCTTCCGGCAACTTTGGGTACCATTGTAAGCTACTTATCATCTGAAGTAACACGTGGCATATGGAAGCCTGCTTTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattacacactgattttgacgtgttacttagatctttgcactattctatttcagGGCTTAAAGACCTTTCTGATTTTCTTCCTGCTTCTTTGGCAACCATTGCAAGTTACTTTTCTGCTGAAGTAACACGCGGTATTTGGAAACCAGCTTTTAT
              ttttgac  putative branch site (score: 3)
                                            ttctatttc  putative PPT
                                          tattctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaatgattgtatgcaggctctcaccttctgtttaaattttggacatattacacactgattttgacgtgttacttagatctttgcactattctatttcagGGCTTAAAGACCTTTCTGATTTTCTTCCTGCTTCTTTGGCAACCATTGCAAGTTACTTTTCTGCTGAAGTAACACGCGGTATTTGGAAACCAGCTTTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
gaaatga
- - - - -gtatgca
- - - - - - - - - ctctcac
- - - - - - - - - - - - -cttctgt
- - - - - - - - - - - - - - - - - - - - - - - - -tacacac