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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacttctgttggcctggcagacaatttattgtgtgttatatttatttttcttattgcccgatttgcttcttaatatttagGTTGAACATGTGAAGGCTGAGAGGAATTTACTTGCAGAGGTTGATAGCAATTGCATTGTCAAACTTTATTGTTCATTCCAAGATGAAGAGTTTCTTTATC

Basic information

species Vitis vinifera
transcript Vv05s0049g01220.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 3
-gtatgacttctgttggcctggcagacaat-ttattgtgtgttatat-ttatttttcttattgcccgatttgcttcttaatatttagGTTGAACATGTGAAGGCTGAGAGGAATTTACTTGCAGAGGTTGATAGCAATTGCATTGTCAAACTTTATTGTTCATTCCAAGATGAAGAGTTTCTTTATC
  ||  |  ||    || || ||   || | |||   ||  |  | | || ||    | ||||     |||   ||    | |||||||||||||||| || |||||||||||| |||||||||| |||||||||||||||||||| || ||||||| ||| || |||||||||||||   | ||||
gttacaaaatcatcaggacttgctctcattgttaaaatgaatattgtcttgttaaattcattggttactttctatccc--tgtttagGTTGAACATGTAAAAGCTGAGAGGAATCTACTTGCAGAAGTTGATAGCAATTGCATTGTAAAGCTTTATTATTCCTTTCAAGATGAAGAGTACTTATATC

upper sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 3
gta-tgacttctgttggcctggcagacaattt---attgtgtgttatatttatttttcttattgcccgatttgcttcttaatatttagGTTGAACATGTGAAGGCTGAGAGGAATTTACTTGCAGAGGTTGATAGCAATTGCATTGTCAAACTTTATTGTTCATTCCAAGATGAAGAGTTTCTTTATC
|||   |  |  |  || || ||   || |||   | ||  | || |  || || |  | ||||     |||   ||    | |||||||||||||||| || |||||||||||| |||||||||| ||||| ||||| |||||||| || ||||||||||| || ||||||||||||| | | ||||
gtaacaaaataagcaggacttgctctcatttttaaaatgaatattgt-cttgttatattcattgattactttttatccc--tgtttagGTTGAACATGTAAAAGCTGAGAGGAATCTACTTGCAGAAGTTGACAGCAACTGCATTGTAAAGCTTTATTGTTCCTTTCAAGATGAAGAGTATTTATATC

upper sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 4
gtatgacttctgttggcctggcagacaatttattgtgtgttatatttatttttcttattgcccgatttgcttcttaatatttagGTTGAACATGTGAAGGCTGAGAGGAATTTACTTGCAGAGGTTGATAGCAATTGCATTGTCAAACTTTATTGTTCATTCCAAGATGAAGAGTTTCTTTATC
           ||     |  || |   ||       |  | ||| |||| || |  |   |  ||| | | |   |  || ||||||||||||| || |||||||| ||| ||||||| || ||||| |||||||||||||| |||||||||||||| || |||||||| |||||| | ||||
-----------gtgaaattatcacattgttagagacttagtgtatatattgttttcttatacttattggatac---actttcagGTTGAACATGTCAAAGCTGAGAGAAATCTACTTGCTGAAGTTGACAGCAATTGCATTGTAAAACTTTATTGTTCCTTTCAAGATGAGGAGTTTTTATATC

upper sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 3
gtatgacttctgttggcctggcagacaatttattgtgtgttatatttatttttct-tattgcccgatttgcttcttaatatttagGTTGAACATGTGAAGGCTGAGAGGAATTTACTTGCAGAGGTTGATAGCAATTGCATTGTCAAACTTTATTGTTCATTCCAAGATGAAGAGTTTCTTTATC
   |||  | | |     ||  |||  | |||  ||   |  | |||  || | | |||||   |||   ||| ||     | ||||||||||||| || |||||||| ||| ||||||| || ||||| |||||||||||||| |||||||||||||| || |||||||| |||| | | ||||
--gtgaaat-tatcacattgttaga-gacttagagtaaatattgttttcttatatgtattg---gatacacttttt-----tcagGTTGAACATGTCAAAGCTGAGAGAAATCTACTTGCTGAAGTTGACAGCAATTGCATTGTTAAACTTTATTGTTCCTTTCAAGATGAGGAGTATTTATATC

upper sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 4
gtatgacttctgttggcctggcagacaatttattgtgtgttatatttatttttcttattgcc--cgatttgcttcttaatatttagGTTGAACATGTGAAGGCTGAGAGGAATTTACTTGCAGAGGTTGATAGCAATTGCATTGTCAAACTTTATTGTTCATTCCAAGATGAAGAGTTTCTTTATC
          | ||    |  |    | |   ||  || | | |||| |||   |  |||      || ||     | || || |||| |||||||| || || ||||| |||||||||||||| |||||||||||||||||||||||||| |||||||| ||||||||||||||||   | ||||
---------gtatttaaattccttcaagtggctttcgtttgacatttgtttagttggttgatgtgaatgtggaatctgattttcagGTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAATTGCATTGTCAAACTGTATTGTTCTTTCCAAGATGAAGAGTACTTGTATC

upper sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgacttctgttggcctggcagacaatttattgtgtgttatatttatttttcttattgcccg-atttgct----tcttaatattt---agGTTGAACATGTGAAGGCTGAGAGGAATTTACTTGCAGAGGTTGATAGCAATTGCATTGTCAAACTTTATTGTTCATTCCAAGATGAAGAGTTTCTTTATC
           ||    |   ||  |   || |||| || ||||| | | ||| |||| |  |   |||| |    ||| | | |||   |||| || |||||||| || ||||| |||||||||||||||||||| |||||||||||||| || || |||||||| || ||||||||||||| | | ||||
-----------gtatctccttcaagctgctt-ttgtttgatatatctttgtttattatcgttcatgtttgttgaaatctgattctttttcagGTGGAGCATGTGAAAGCAGAGAGAAATTTACTTGCAGAGGTTGACAGCAATTGCATTGTGAAGCTGTATTGTTCTTTTCAAGATGAAGAGTATTTGTATC

upper sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 3
---------gtatgacttctgttggcctggcagacaattt-attgtgtgttatatttatttttcttattgcccgatttg----cttcttaatattt--agGTTGAACATGTGAAGGCTGAGAGGAATTTACTTGCAGAGGTTGATAGCAATTGCATTGTCAAACTTTATTGTTCATTCCAAGATGAAGAGTTTCTTTATC
         | ||||   |  |     ||  | | | ||| || |  | | ||| | |    || ||      || |||     ||     || ||  |||| || ||||| || || ||||| ||||| ||||||||||| ||||||||||| ||||| ||  | ||||| || || |||||||| |||| | | ||| 
tcatcataagaatgataacaataataatgataaatatttttatcgactatgatagtgaaaaatcatagccattgaattgaaaattttgcggtaattgcagGTGGAGCATGTAAAAGCAGAGAGAAATTTGCTTGCAGAGGTCGATAGCAATTGTATTGTGAAGTTGTATTGCTCGTTTCAAGATGAGGAGTATTTGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgtgtgttatatttatttttcttattgcccgatttgcttcttaatatttagGTTGAACATGTGAAGGCTGAGAGGAATTTACTTGCAGAGGTTGATAGCAATTGCATTGTCAAACTTTATTGTTCATTCCAAGATGAAGAGTTTCTTTATC
                                          tcttaat  putative branch site (score: 3)
                                    tttgcttctt  CT-rich tract
      tgtgttatatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgacttctgttggcctggcagacaatttattgtgtgttatatttatttttcttattgcccgatttgcttcttaatatttagGTTGAACATGTGAAGGCTGAGAGGAATTTACTTGCAGAGGTTGATAGCAATTGCATTGTCAAACTTTATTGTTCATTCCAAGATGAAGAGTTTCTTTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA