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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacgtagaaggagctttatagcattatgccgcccattttagtttctccattattgcaaatttaggttgctcttgtaacttatttccgttcatttttgtagCAAGCCAAGTGCACCCGAAGAATTGGTATCCAATTCCACTGGTATTTTGCCGACCCTGGGGCAAACTGCCAGAAAATGTTCCCTGTCATCCCAAACTTGC

Basic information

species Glycine max
transcript GLYMA15G22520.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 13
cacgtagaaggagctttatagcattatgccgcccattttagtttctccattattgcaaatttaggttgctcttgtaacttatttccgttcatttttgtagCAAGCCAAGTGCACCCGAAGAATTGGTATCCAATTCCACTGGTATTTTGCCGACCCTGGGGCAAACTGCCAGAAAATGTTCCCTGTCATCCCAAACTTGC
   ||| ||    |||  | | |     |     ||  ||  ||    | ||||  | | |||  ||| |  |   ||| |    | ||| || |   ||||| ||||||||| || ||||||||||| || ||||| ||| |||| ||||| || ||||| ||||| ||||||||||| || |||||||| || |||||
---gtataactctcttcttggaa----actaaatatcata--tttgaaactatta-agagttaccttgtttgtaacactgaa---cattc-ttgtcacagCAAACCAAGTGCATCCTAAGAATTGGTACCCCATTCCTCTGATATTCTGCCGTCCTTGGGGTAAACTTCCAGAAAATGTACCTTGTCATCCAAAGCTTGC

upper sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G113276_T01 (Zea mays), 3'ss of exon 7
cacgtagaaggagctttatagcattatgccgcccatt-ttagtttctccattattgcaaatttaggttgc--tcttgtaacttatttccgttcatttttgtagCAAGCCAAGTGCACCCGAAGAATTGGTATCCAATTCCACTGGTATTTTGCCGACCCTGGGGCAAACTGCCAGAAAATGTTCCCTGTCATCCCAAACTTGC
                          ||| ||  | | |  | ||  | |||| |  ||   ||  |  |  | |||||||||      | || ||| || ||||| |||||| || || ||||||||||| || ||||| ||| |||| ||||| || |||||||||||||| ||||||||||| |||||||| ||||||||
-------------------------gtgcggctgactatctgctttgcaattact-taatcatacttaacaattttgtaactt-----tggtcctttctgcagCAAACCAAGTCCATCCTAAGAATTGGTACCCCATTCCTCTGATATTCTGCCGTCCATGGGGCAAACTGCCGGAAAATGTTCCTTGTCATCCAAAACTTGC

upper sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G449569_T01 (Zea mays), 3'ss of exon 1
cacgtagaaggagctttatagcattatgccgcccattttagtttctccattattgcaaatttaggttgctcttgtaacttatttccgttcatttttgtagCAAGCCAAGTGCACCCGAAGAATTGGTATCCAATTCCACTGGTATTTTGCCGACCCTGGGGCAAACTGCCAGAAAATGTTCCCTGTCATCCCAAACTTGC
                          | |  |  | | |   | ||     | | || | |        | ||||||| | |    | || ||| || ||||| |||||| || || ||||||||||| || ||||| |||||||| ||||| || ||||| ||||| || ||||||||||| |||||||| ||||||||
-------------------------gtacgactgactat--ctgctttgcgaatacataatcgtacaatt-ttgtaaccttt----ggtcctttctgcagCAAACCAAGTCCATCCTAAGAATTGGTACCCCATTCCTCTGGTATTCTGCCGTCCATGGGGTAAACTTCCGGAAAATGTTCCTTGTCATCCAAAACTTGC

upper sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 12
--cacgtagaaggagctttatagcattatgccgcccattttagtttctccattattgcaaatttaggttgctcttgtaacttatttccgttcatttttgtagCAAGCCAAGTGCACCCGAAGAATTGGTATCCAATTCCACTGGTATTTTGCCGACCCTGGGGCAAACTGCCAGAAAATGTTCCCTGTCATCCCAAACTTGC
      |      | |||| |  | |      |    | |||  |   |   | ||  |     |   || |||| | | |||  ||   | || | || |||||||||||||||||| ||||| |||||||| ||||| ||  |||| ||||| || ||||| || |||||||| ||||| ||||| || || ||| | ||
tttttctctctctacctttttcccttgcctgtgtgtttattatatatgcatgttttatatgaacatcatgttcttattatttacctc--attatatgtgcagCAAGCCAAGTGCACCCAAAGAACTGGTATCCTATTCCCCTCATATTCTGCCGGCCATGGGGGAAGCTGCCAGAGAATGTGCCCTGCCACCCTAAATTAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccattattgcaaatttaggttgctcttgtaacttatttccgttcatttttgtagCAAGCCAAGTGCACCCGAAGAATTGGTATCCAATTCCACTGGTATTTTGCCGACCCTGGGGCAAACTGCCAGAAAATGTTCCCTGTCATCCCAAACTTGC
                          ttgtaac  putative branch site (score: 2)
                                    tttccgttcattttt  putative PPT
                             taacttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacgtagaaggagctttatagcattatgccgcccattttagtttctccattattgcaaatttaggttgctcttgtaacttatttccgttcatttttgtagCAAGCCAAGTGCACCCGAAGAATTGGTATCCAATTCCACTGGTATTTTGCCGACCCTGGGGCAAACTGCCAGAAAATGTTCCCTGTCATCCCAAACTTGC

- - - - - - - - - - - - - - -cgcccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggttgc