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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgaaattcctgtagaagttagtttttgtttcttttttggttatcatgtttgcgatctgaccattccttcttgttttccttttcagAGCGTGCCGAACGGGTAATTTTATTGCCTTCTTTCGGCTTGCAAGAAAAGCAACTTATCTTCAAGCATGCCTAATGCATGCTCACTTTGCTAAG

Basic information

species Glycine max
transcript GLYMA15G10760.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G10760.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g45160.1 (Oryza sativa), 3'ss of exon 13
gttgaaattcctgtagaagttagtttttgtttcttttttggttatcatgtttgcgatctgaccattccttcttgttttccttttcagAGCGTGCCGAACGGGTAATTTTATTGCCTTCTTTCGGCTTGCAAGAAAAGCAACTTATCTTCAAGCATGCCTAATGCATGCTCACTTTGCTAAG
   | | |     ||     |  | |||||   | |   | | ||    |||| ||| | ||   |  ||    | || |  |||||||| ||||||| ||| || ||||||||||||||||| |||||||| |||||||| ||  | || || ||  | ||||||||||||||||| |||
---gtagtcatactatctacttttgtttgtacttatcaagttcattg-atttgtgatttaacaccttttttccctattgccattcagAGCTTGCCGAATGGGGAACTTTATTGCCTTCTTTCGTCTTGCAAGGAAAGCAACATACTTGCAGGCTTGTTTGATGCATGCTCACTTTGCAAAG

upper sequence: GLYMA15G10760.2 (Glycine max), 3'ss of exon 6
lower sequence: AT3G06290.1 (Arabidopsis thaliana), 3'ss of exon 14
gttgaaattcctgtagaagttagtttttgtttcttttttggttatcatgtttgcgatctgaccattccttcttgttttccttttcagAGCGTGCCGAACGGGTAATTTTATTGCCTTCTTTCGGCTTGCAAGAAAAGCAACTTATCTTCAAGCATGCCTAATGCATGCTCACTTTGCTAAG
   | | ||||| | ||  ||  ||||||||   | || | || | |  ||   ||||| |  |||    |  ||  | |    |||||| ||| |||| || || || || ||||||||||| |||||| | |||||||  |||||||||||||| |||||||||||||| ||| | || 
---gtagttcct-tgga--tt--tttttgttggctgttagttttttaactt---gatctaagtattgaaaccagtcgtgcaaaacagAGCTTGCAGAACTGGCAACTTCATCGCCTTCTTTCGCCTTGCACGGAAAGCAAGCTATCTTCAAGCATGTCTAATGCATGCTCATTTTTCGAAA

upper sequence: GLYMA15G10760.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0020g02350.t01 (Vitis vinifera), 3'ss of exon 9
gttgaaattcctgtagaagttagtttttgttt-cttttttggttatcatgtttgcgatctgaccattccttcttgttttcctt--ttcagAGCGTGCCGAACGGGTAATTTTATTGCCTTCTTTCGGCTTGCAAGAAAAGCAACTTATCTTCAAGCATGCCTAATGCATGCTCACTTTGCTAAG
            ||     |    ||   |   ||| |  ||||      ||    |      |||       || ||  |||  | |||||| ||| ||||  ||||||| ||||| |||||||||||||  |  ||||||| ||||||||||||||||||||||||||||||||||||||||
------------gtttgcctccccttaaatccacttgtcaggttgaagcattgaacagaatctcatattagagtgattgtcttcatgcagAGCTTGCAGAACAAGTAATTTCATTGCTTTCTTTCGGCTTGGGAAGAAAGCAAGTTATCTTCAAGCATGCCTAATGCATGCTCACTTTGCTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttttggttatcatgtttgcgatctgaccattccttcttgttttccttttcagAGCGTGCCGAACGGGTAATTTTATTGCCTTCTTTCGGCTTGCAAGAAAAGCAACTTATCTTCAAGCATGCCTAATGCATGCTCACTTTGCTAAG
                       atctgac  putative branch site (score: 3)
                        tctgaccattccttct  CT-rich tract
         ttatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgaaattcctgtagaagttagtttttgtttcttttttggttatcatgtttgcgatctgaccattccttcttgttttccttttcagAGCGTGCCGAACGGGTAATTTTATTGCCTTCTTTCGGCTTGCAAGAAAAGCAACTTATCTTCAAGCATGCCTAATGCATGCTCACTTTGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA