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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttttgcatcaattgtaacaaatgatttgtatttactgtattgcccagctatctctctcccatgtgccattgaaaggttttaatatattgaataacagGTGCGGGCAACTGCTAGAATGTGCTACAGAATGTTTGCAAAAACTTGGCCGGATCGTTCTCGCCGGTTGTTTTCGTCCTTTGACCCTGTCATTCAAAGG

Basic information

species Arabidopsis thaliana
transcript AT2G20190.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 11
atgttttgcatcaattgtaacaaatgatttgtatttactgtattgcccagctatctctctcccatgtgccattgaa--aggttttaatatattg----aataacagGTGCGGGCAACTGCTAGAATGTGCTACAGAATGTTTGCAAAAACTTGGCCGGATCGTTCTCGCCGGTTGTTTTCGTCCTTTGACCCTGTCATTCAAAGG
    | | |    | ||| | |||   ||   ||||| |||  |       |   |   | |  | |   |||       |||| | | ||||     ||    ||||  |||||||||| ||||  ||||| |||||||||||||| || ||||| || ||||| |||||  | |||  ||  ||||| ||||  || || |||
----tctactggtactgtgagaaa--gttcacatttattgtgatcattgatttagttcatacattttaagattattttgtgtttcattgtatttcctcaactctagGTTAGGGCAACTGCAAGAACTTGCTATAGAATGTTTGCAAAGACATGGCCTGAGCGTTCACGCCGTCTTTTTATGTTATTTGATCCTGCGATACAGAGG

upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA03G32710.1 (Glycine max), 3'ss of exon 11
---atgttttgcatcaattgtaacaaatgatttgtatttactgtattgcccagctatctctctcccatgtgccattgaaaggttttaatatattgaa--taacagGTGCGGGCAACTGCTAGAATGTGCTACAGAATGTTTGCAAAAACTTGGCCGGATCGTTCTCGCCGGTTGTTTTCGTCCTTTGACCCTGTCATTCAAAGG
      |||| |||  ||| ||  | |  |   || ||||   ||||       |||         || ||  | |||||    ||| | | |  ||  ||| |||| ||| | ||||| || |||||||||||||||||||||||||||||||| || |||||||| ||  | ||||| |||||||||||||  |||||| ||
ttatcatttttcattgatt-taggacagaaa--gtctttagcatattcattgattattcaaagt--atatggaagtgaaaataattactgtgtgaaaattaatagGTACGGTCTACTGCAAGGATGTGCTACAGAATGTTTGCAAAAACTTGGCCAGAGCGTTCTCGTCGCCTATTTTCATCCTTTGACCCTGCGATTCAACGG

upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA19G35460.1 (Glycine max), 3'ss of exon 11
---atgttttgcatcaattgtaacaaatgatttgtatttactgtattgcccagctatctctctcccatgtgccattgaaaggttttaatatattgaataacagGTGCGGGCAACTGCTAGAATGTGCTACAGAATGTTTGCAAAAACTTGGCCGGATCGTTCTCGCCGGTTGTTTTCGTCCTTTGACCCTGTCATTCAAAGG
      |||| |||  |||      |   | |  |   ||   || |       |||         |||        ||   ||   ||||    | ||| |||| ||| | ||||| || |||||||||||||||||||| ||||||||||| || |||||||| ||  | ||||| |||||||||||||  |||||| ||
tcatcatttttcattgatttaggacagaaactcat---tagcatactcattgattattcaaagtatatgcatgtgaaaataattactatatgaaaattaatagGTACGGTCTACTGCAAGGATGTGCTACAGAATGTTTGCCAAAACTTGGCCTGAGCGTTCTCGTCGCCTATTTTCATCCTTTGACCCTGCTATTCAACGG

upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA10G04850.1 (Glycine max), 3'ss of exon 11
-atgttttgcatcaattgtaacaaatgatttgtatttactgt-attgcccagctatctctctcccatgtgccattgaaaggttttaatatattgaataacagGTGCGGGCAACTGCTAGAATGTGCTACAGAATGTTTGCAAAAACTTGGCCGGATCGTTCTCGCCGGTTGTTTTCGTCCTTTGACCCTGTCATTCAAAGG
    | ||   | | |||  |    | || ||    || |||   |||| ||  ||   |     | ||||     ||   ||  ||||  |    | | |||||||| | ||||| || ||||| ||||||||||||||||| |||||||| || ||||| || ||  ||||||| || ||||||||||  |||||||||
agcatatttgttgacttgacatttttcatgtggccgtattgttggtgccaagtaataagtgcaata-gtgcataaaaataattacaatac-taacttgatagGTGCGGTCGACTGCAAGGATGTGTTACAGAATGTTTGCAAAGACTTGGCCAGAACGTTCCCGTCGCCTGTTTTCATCATTTGACCCTGCTATTCAAAGG

upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G19230.1 (Glycine max), 3'ss of exon 11
atgttttgcatcaattgtaacaaatgatttgtatttactgtattgcccagctatctctctcccatgtgccattgaaaggttttaatatattgaa--taacagGTGCGGGCAACTGCTAGAATGTGCTACAGAATGTTTGCAAAAACTTGGCCGGATCGTTCTCGCCGGTTGTTTTCGTCCTTTGACCCTGTCATTCAAAGG
  | ||  || ||  | |    | |      | || |       ||   | |    |       |  |    | |||    |||   |||| ||  | | |||||||| | ||||| || ||||| ||||||||||||||||| |||||||| || ||||| || ||  ||||||| || ||||||||||  |||||||||
--gcttgtcagcatatttgttgacttgacatttttcatgtggccgcattgttggtgccaagttgtaagtgcataaaaataattacagtattaaacttgatagGTGCGGTCGACTGCAAGGATGTGTTACAGAATGTTTGCAAAGACTTGGCCAGAACGTTCCCGTCGCCTGTTTTCATCATTTGACCCTGCTATTCAAAGG

upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 8
atgttttgcatcaattgtaacaaatgatttgtatttactgtattgcccagctatctctctccc--atgtgccattgaaaggttttaatatattgaa---taacagGTGCGGGCAACTGCTAGAATGTGCTACAGAATGTTTGCAAAAACTTGGCCGGATCGTTCTCGCCGGTTGTTTTCGTCCTTTGACCCTGTCATTCAAAGG
     ||| ||   || |   ||||   ||  ||  |   |||       ||     | |||   | |   |||   | |   |||| | | ||||    |||||||  |   |||||| || |||||||||||||||||||||||||||||||| || ||||| || || || |||  || |||||| ||||| |||||||||
----attgaatatgtttttcaaaatttattccatg-atgatatcctgtgactggtaatgtccttaaaggttcatcatatgaacttaacaaactgaaactcaacagGTAAGACTAACTGCCAGGATGTGCTACAGAATGTTTGCAAAAACTTGGCCAGAGCGTTCCCGGCGCTTATTTGTGTGCTTTGATCCTGTTATTCAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccagctatctctctcccatgtgccattgaaaggttttaatatattgaataacagGTGCGGGCAACTGCTAGAATGTGCTACAGAATGTTTGCAAAAACTTGGCCGGATCGTTCTCGCCGGTTGTTTTCGTCCTTTGACCCTGTCATTCAAAGG
                                  ttttaat  putative branch site (score: 3)
                         attgaaaggttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttttgcatcaattgtaacaaatgatttgtatttactgtattgcccagctatctctctcccatgtgccattgaaaggttttaatatattgaataacagGTGCGGGCAACTGCTAGAATGTGCTACAGAATGTTTGCAAAAACTTGGCCGGATCGTTCTCGCCGGTTGTTTTCGTCCTTTGACCCTGTCATTCAAAGG

-tgttttg
- - - - - - - - -taacaaa
- - - - - - - - - - - - -gatttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttta