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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaattacctgtgaaccatgatcctacattaactaaaaccatttgaccttttaacgactttattctatcctcccactaaattctttttttttttctctagAGAAGAGGAAGAGCTGGTCGTGTTCAACCAGGAGAATGTTATCATCTCTATCCTAGATGTGTATATGATTCTTTTGCAGAGCATCAATTACCTGAAATTT

Basic information

species Glycine max
transcript GLYMA09G18490.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G18490.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------------------------------------gcaatta-cctgtgaaccatgatcctacattaactaaaaccatttgaccttttaacgactttattctatcctccca-ctaaattctttttttttttctctagAGAAGAGGAAGAGCTGGTCGTGTTCAACCAGGAGAATGTTATCATCTCTATCCTAGATGTGTATATGATTCTTTTGCAGAGCATCAATTACCTGAAATTT
                                                                       | ||| |   ||  ||  |  ||  |   ||||||  ||| |         | |||   | |||  |||| |     |||| |   || | |     | |||||| |||||||||||||||| || |||||||| || ||||| ||||| |||||   ||| || |||||  | ||||| ||  |||| || || ||| |  
gtgtttttctcttgttggagtattactaattttatttttttcgtaacactttgaatgaatttgcattttctggaatcaatatgctaataaatatttttttttaactttaac-acgcatatcatcaac--ttctatcatatcattttggctaattaaattgtataacaatttagAGACGAGGAAGAGCTGGTCGAGTCCAACCAGGGGAGTGTTACCATCTATATCCACAATGCGTGTATGAAGCATTTGCTGACTATCAGTTGCCAGAACTCC

upper sequence: GLYMA09G18490.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G01130.1 (Arabidopsis thaliana), 3'ss of exon 11
gcaattacctgtgaaccatgatcctacattaactaaa-accatttgaccttttaacgactttattctatcctcccactaaattctttttttttttctctagAGAAGAGGAAGAGCTGGTCGTGTTCAACCAGGAGAATGTTATCATCTCTATCCTAGATGTGTATATGATTCTTTTGCAGAGCATCAATTACCTGAAATTT
  || ||        | |  ||| || | || || |        ||  |||  |   | |    | |||  |        || || | ||| |   |  |||||||||||||||| |||||||||| ||| ||| | ||||| ||||| || || |  || ||||||||| ||||||||||  |||| || ||||||||||
ataagtattcactgccaacaatctta-actatctgactggtccgtgggcttacatttagtgatatttattgttgattctcatgctctgtttgtgattgcagAGAAGAGGAAGAGCCGGTCGTGTTCGACCTGGACAGTGTTACCATCTTTACCCAAAGTGCGTATATGATGCTTTTGCAGAATATCAGTTGCCTGAAATTT

upper sequence: GLYMA09G18490.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0011g04360.t01 (Vitis vinifera), 3'ss of exon 11
gcaattacctgtgaaccatgatcctacattaactaa-aaccatttgaccttttaacgactttattctatcctcccactaaattctttttttttttctctagAGAAGAGGAAGAGCTGGTCGTGTTCAACCAGGAGAATGTTATCATCTCTATCCTAGATGTGTATATGATTCTTTTGCAGAGCATCAATTACCTGAAATTT
   ||| | |   ||  |   |     |  || ||  || ||   |    ||  |    |||  | |||  |||      || |||| | |  |  | |||||||||||||||||||| ||||||||||||||| ||||||| |||||||||||| |||||||||||||| ||||||||||  ||||||| ||||||||||
ctgattccttccaaattacattgacttagaaaataggaatcaagggtttattgcatatgtttgatatattttcctttcctatgctttgtctaata-tgtagAGAAGAGGAAGAGCTGGCCGTGTTCAACCAGGAAAATGTTACCATCTCTATCCTCGATGTGTATATGATGCTTTTGCAGATTATCAATTGCCTGAAATTT

upper sequence: GLYMA09G18490.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ13473 (Selaginella moellendorffii), 3'ss of exon 11
gcaattacctgtgaaccatgatcctacattaactaaaaccatttgaccttttaacgactttattctatcctcccactaaattctttttttttttctctagAGAAGAGGAAGAGCTGGTCGTGTTCAACCAGGAGAATGTTATCATCTCTATCCTAGATGTGTATATGATTCTTTTGCAGAGCATCAATTACCTGAAATTT
                                                 | ||       |  |||||       |   |||||   || | |  |  || |  |||||||||| || |||||  | ||||| |||||||||||||||||||| |     ||  | ||  | ||||| ||  ||||  | || ||  || 
------------------------------------------------gtatactcttgcttctctatggaaatgcgttattctaacttctgtcttgcagCGTCGAGGAAGAGCAGGACGTGTAAAGCCAGGGGAATGTTATCATCTCTATCCCAAGGCCGTTCACGAAGCATTTGCGGAATATCAGCTGCCGGAGCTTC

upper sequence: GLYMA09G18490.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ19043 (Selaginella moellendorffii), 3'ss of exon 11
gcaattacctgtgaaccatgatcctacattaactaaaaccatttgaccttttaacgactttattctatcctcccactaaattctttttttttttctctagAGAAGAGGAAGAGCTGGTCGTGTTCAACCAGGAGAATGTTATCATCTCTATCCTAGATGTGTATATGATTCTTTTGCAGAGCATCAATTACCTGAAATTT
                                                 | ||       |  |||||       |   |||||   || | |  |  || |  |||||||||| || |||||  | ||||| |||||||||||||||||||| |     ||  | ||  | ||||| ||  ||||  | || ||  || 
------------------------------------------------gtatactcttgcttctctatggaaattcgttattctaacttctgtcttgcagCGTCGAGGAAGAGCAGGACGTGTAAAGCCAGGGGAATGTTATCATCTCTATCCCAAGGCCGTTCACGAAGCATTTGCTGAATATCAGCTGCCGGAGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttttaacgactttattctatcctcccactaaattctttttttttttctctagAGAAGAGGAAGAGCTGGTCGTGTTCAACCAGGAGAATGTTATCATCTCTATCCTAGATGTGTATATGATTCTTTTGCAGAGCATCAATTACCTGAAATTT
                            cactaaa  putative branch site (score: 2)
                 ttctatcctcccacta  CT-rich tract
                               taaattcttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaattacctgtgaaccatgatcctacattaactaaaaccatttgaccttttaacgactttattctatcctcccactaaattctttttttttttctctagAGAAGAGGAAGAGCTGGTCGTGTTCAACCAGGAGAATGTTATCATCTCTATCCTAGATGTGTATATGATTCTTTTGCAGAGCATCAATTACCTGAAATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - -cctgtga
- - - - - - - - catgatc
- - - - - - - - - - - -ctacatt
- - - - - - - - - - - - - - - - - - - ccatttg