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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTGgtaattttcttccatataaatttcctattttgtagttagtaaatagcctctctttttttactgaatttgttatttttgttatgcag

Basic information

species Glycine max
transcript GLYMA03G12240.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G12240.1 (Glycine max), 5'ss of exon 13
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 12
CTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTGgtaa-ttttcttccatataaatttccta----ttttgtag--ttagtaaatagcctctctttttttactgaatttgttatttttgttatgcag----------------
||||||||||| || ||||| ||  | || ||||| |||||||||||||| |||||||||||||  ||||| || |||||||||||||| ||||||||||| || | ||  |  | || ||| ||    | || | |  ||| |  ||      | |||||||  |   |||| ||||| ||  || |                  
CTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTGgtaaattctgtttgaacttaagttcttaccactcttatggctttattggatgttgagtttttttttctt---tttgctatttctgacattccatatttccccactgcag

upper sequence: GLYMA03G12240.1 (Glycine max), 5'ss of exon 13
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 5'ss of exon 13
CTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTGgtaa--ttttcttccatataaatttcctattt-----tgtagttagta----aatagcctctctttttt-------------tactgaatttgttatttttgttatgcag--------------------------------
||||||||||| || ||||| ||  | || ||||| || |||||||| ||||| || ||||| | | |||| || ||||||||||||||||||||||||||  || | ||   |||  | ||| | |       | |   |||||    ||| |    |  ||||              || |  ||||  | ||||| |||||                                   
CTTGATGATGTGATTGATCTTGTAATACCAAGAGGTAGCAATAAGCTCGTTTCCCAGATCAAAGCAGCAACCAAGATTCCTGTTCTTGGTCATGCTGgtaagcttgtttttgttattgaattcttgtcactaaatattactagtatgataatggttatttattttgcataaactaagcataatacatttcctttttttattatgatatacattgaatgaatgttttttttcttctacag

upper sequence: GLYMA03G12240.1 (Glycine max), 5'ss of exon 13
lower sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 12
CTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTGgtaatttt--cttccatataaatttcctattttgtag---ttagtaaatagcctctctttttttactgaatttgtt-----atttttgttatgcag
||| |||||||||| ||||| ||  | || |||||||| |||||||| ||||| |||||||||  |||||| || || ||||||||||||||||||||||| |||  ||||||     || |  |  |    |    | | || |    |    | |    |||   ||  ||     || |||  | |  ||
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaatttatcttccaatagcatgttttggtacaaacatttcactacaatatcaaaatatgcagactagtttgatttctgaatctttcctctatag

upper sequence: GLYMA03G12240.1 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G094309_T01 (Zea mays), 5'ss of exon 5
CTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTGgtaatttt--cttccatataaatttcctattttgtag---ttagtaaatagcctctctttttttactgaatttgtt-----atttttgttatgcag
||| |||||||||| ||||| ||  | || ||||| || |||||||| ||||| |||||||||| |||||| || || ||||||||||||||||||||||| |||  ||||||     || |  |  |    |    | | || |    |    | |    |||   ||  ||     || |||  | |  ||
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGTAGCAATAAGCTGGTTTCACAAATCAAGGCATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaatttatcttccaatagcatgttttggtacaaacatttcactacaatatcaaaatatgcagactagtttgatttctgaatctttcctctatag

upper sequence: GLYMA03G12240.1 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G375504_T03 (Zea mays), 5'ss of exon 12
CTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTGgtaa--ttttcttccatataaatttcctattttgtagttagtaaatagcctctctt-----tttttactgaatttgtt-----atttttgttatgcag
||||||||||| || ||||| ||  | || |||||||| |||||||| ||||| |||||||| | |||||| || || ||||| || |||||||| |||||  || ||||||| |||  ||   | |  |  |   |||  |   |    ||      |    ||||  ||  ||     ||||||  | |  ||
CTTGATGATGTCATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCGCAAATCAAAGCATCAACTAAGATACCTGTCCTCGGTCATGCGGgtaaatttatcttcca-atagtttgtttttggtacaaacagtccactacaatactaaaatatacggactggtttgatttctgaattttttctctatag

upper sequence: GLYMA03G12240.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv08s0007g01060.t01 (Vitis vinifera), 5'ss of exon 13
CTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTGgtaattttcttccatataaatttcctattttgtagttagtaaatagcctctctttttttactgaatttgttatttttgttatgcag
||||||||||| |||||||| ||| ||||||||||||| || || || ||||||||||||||||| ||||| ||||| |||||||||||||||||||||||  |   |   | | | | |   | ||| || |  | |||       | || || || ||  |||| | |             
CTTGATGATGTCATAGATCTTGTGATCCCTAGAGGCAGCAACAAACTCGTTTCTCAAATCAAGGATTCAACTAAAATCCCTGTTCTTGGTCATGCTGgtaagataaat---tgtgactctttaaatttataatctgcaaactagaggttttattatagtg--tttgctttcag----------

upper sequence: GLYMA03G12240.1 (Glycine max), 5'ss of exon 13
lower sequence: EFJ29127 (Selaginella moellendorffii), 5'ss of exon 13
CTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTGgtaattttcttccatataaatttcctattttgtagttagtaaatagcctctctttttttactga-atttgttatttttgttatgcag
||||| ||||| || || || ||  | || ||||| || ||||| |||||||| ||||||||||| || || ||||||||||| || || ||||| ||||   | |||   |       |         | ||      || ||      | |||  |||| |  ||  |      |||     
CTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCGgtatgctacttttgtcctcgcattgcgaaagtttgtcctcgcattgcgaaagctgttt--ctgacacatggaaaaccctttag----

upper sequence: GLYMA03G12240.1 (Glycine max), 5'ss of exon 13
lower sequence: EFJ17662 (Selaginella moellendorffii), 5'ss of exon 13
CTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTGgta----attttcttccatata-----aatttcctattttgtagttagtaaatagcctctctttttttactgaattt----gttatttttgttatgcag------
||||| ||||| || || || ||  | || ||||| || ||||| |||||||| ||||||||||| || || ||||||||||| || || ||||| ||||    | |||  |||    |     ||  |      | |   |  | ||   |  |||      |     |  ||     |  | | ||  |||         
CTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCGgtatgctacttttgtcctcgcattgcgaaaatttgtcctcgcgttgcgaaagctgtttctgacacatggaaaaccttttagatggtatctgccatgtctacgtag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTGgtaattttcttccatataaatttcctattttgtagttagtaaatagcctctctttttttactgaatttgttatttttgttatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG