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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatgccaatgagctttcttctagcttttgcggattcattgctgatatctactacttactaagtgattctcttgcatttgtgtgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG

Basic information

species Arabidopsis thaliana
transcript AT3G15980.3
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 19
caatgccaatgagctttcttctagcttttgcgga-ttcattgctgatatctact--acttactaagtgattctct-tgcatttgtgtgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG
 |  |  | | |   |  |||| |  |  | | | || | || ||||   |  |  |  |      |||| |  | |   |     | | ||| ||  |   || |  || |||| ||||| ||  ||||||| || |||||||||||||| |||||||| |||||||||||||| ||||||||||||||  | ||||||||||
-agagtaagtaa---tgattctggaatgagggaacttaaatgttgattcttgttggaaatttctcttgatccattgtagctcaccatattttccattgttgcagTTAGAAATGGCTGAGGAATGTTTGAAGTATGCAATGGATTTGAGTGGCTTGTTACTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 19
caatgccaatgagctttc-ttctagcttttgcgga-ttcattgctgatatctactacttac-taagtgattctcttgcatttg--tgtgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG
       ||| || | |  ||||||  |  | | | || | || ||||   |  |    || |   |    |  ||| |  |    || | ||| ||  |   || |  || |||| ||||| ||  ||||||| || |||||||||||||| |||||||| |||||||||||||| ||||||||||||||  | ||||||||||
-----agaataagttatgattctagaatgagggaacttaaatgttgattcttgttggaaacctctcttgacccgttgtagctcaccgtattttccattcttgcagTTAGAAATGGCTGAGGAATGTTTGAAGTATGCAATGGATTTGAGTGGCTTGTTACTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 19
---caatgccaatgagctttcttctagcttttgcggattcattgctgatatctactacttactaagtgattctcttgcatttgtgtgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG
      |     ||       |  ||    ||  |||  || |  |||| |  | |  | |    ||   ||| ||  || | |   |  ||| |  |   || |  || ||||||| || ||  | ||  | || |||||||||||||| || || || |||||||||||||| ||||||||||||||  | ||||||||||
ttcttttattcttgtcacaattaataatgattctggacacact--tgatgttgattggt-atagggtatctcttttttatctcttcattatctgttcttgcagTTAGAAATGGCCGAAGAGTGTTTAAAACAAGCAATGGATTTGAGTGGGTTATTGCTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 8
caatgccaatgagctttcttctagcttttg-cggattcattgctgatatctactacttactaagtgattctcttgcatttg--tgtgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG
   |      |   ||  |  |   | | | |  | |   || ||||   || |   ||        ||  || |||  |   | | |  ||| |  |   || |  || |||| || || ||  | ||  |||| |  ||||||||||| || || || |||||||||||||| ||||||||||||||  | ||||||||||
---tcttgtcgcaattaataatgattctggacacacttgatgttgattggtattgggtatctctctttttcctagcaactcactttattatctgttcttgcagTTAGAAATGGCTGAAGAGTGTTTAAAACACGCAACAGATTTGAGTGGGTTATTGCTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 19
caatgccaatgagctttcttctagc-ttttgcggattcattgctgatat-ctactacttactaagtgattctcttgcatttgtg--tgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG
         |||  |  | |  ||   |||    | | ||  ||  ||   |  |  | | | | | | ||| ||   ||| |   | |||| | | ||   || |  || |||| ||||| ||  | ||| | || ||||| |||||||||||||| || || ||||||||||| ||||||||||| ||  | ||||||||||
----cttcgtgaattacccttcagtgctttagacaattatcacttgtaagtttttgttcattgatttaatcttttttttttttccctctgttatcttattgcagTTAGAAATGGCTGAGGAATGTTTAAAGCATGCGATGGACTTGAGTGGTTTGTTGCTGCTCTATTCTTCTTTAGGAGATGCTGACGGAATATCAAAACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctactacttactaagtgattctcttgcatttgtgtgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG
       tacttac  putative branch site (score: 1)
                                         ttctatc  putative PPT
          ttactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatgccaatgagctttcttctagcttttgcggattcattgctgatatctactacttactaagtgattctcttgcatttgtgtgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG