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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACACAGAGGAGCAGGAGGAACAGAATGGAGAGGAAGGAAGCCAAGAGGAGGCAGTTGTAGTGGATGCAGATTCTACAGATGGTGCAGTACTCGTTAATGgtaacgaggctgacgaagagtggggtacgaataatgaaggagccccgtcagcctaaaagcaattggttggggtggtgtgaaaatcaaaattttgtctctg...

Basic information

species Glycine max
transcript GLYMA13G43680.2
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 24
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 24
TACACAGAGGAGCAGGAGGAACAGAATGGAGAGGAAGGAAGCCAAGAGGAGGCAGTTGTAGTGGATGCAGATTCTACAGATGGTGCAGTACTCGTTAATGgtaacgaggctgacgaagagtggggtacgaataatgaaggagccccgtcagcctaaaagcaattggttggggtggtgtgaaaatcaaaattttgtctctg--------------------------
                        ||   || ||| |  |||  ||| || || || | ||| ||||| |||    | || |   | || || || ||||| || |||| ||| ||| ||||||||||||| ||||||||| |  |||||||||||||| ||||| ||||    |||| |||| | |||||||||||  |                          
------------------------AACAAAGTGGAGGAGAGCACAGATGAAGCTGTCGAAGTTGATGCTGATGAGCCTGAAGAGACCGTTCTTGTAAATGGGAAAGAGGGTGAGGAACAGTGGGgtacgaacaatgaaggaacttcgtcagcctaaaag-aattgtttggca-agtgtaaaaacccaaattttgtctgcggtgattcactagctttgcccccaaat

upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 24
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 24
TACACAGAGGAGCAGGAGGAACAGAATGGAGAGGAAGGAAGCCAAGAGGAGGCAGTTGTAGTGGATGCAGATTCTACAGATGGTGCAGTACTCGTTAATGgtaacgaggctgacgaagagtggggtacgaataatgaaggagccccgtcagcctaaaagcaattggttggggtggtgtgaaaatcaaaattttgtctctg----------------------------------------------------------------------
                                                                     |||    | || |   | || || || ||||| || |||| ||| ||| ||||||||||||| ||||||||| |  |||||||||||||| ||||| ||||    |||| |||| | |||||||||||  |                                                                      
--------------------------------------------------------------------TGATGAGCCTGAAGAGACCGTTCTTGTAAATGGGAAAGAGGGTGAGGAACAGTGGGGTACGAACAATGAAGGAACTTCGTCAGCCTAAAAG-AATTGTTTGgca-agtgtaaaaacccaaattttgtctgcggtgattcactagctttgcccccaaattataggactgttgaacctttctagtacttcagtttttgaaaaag

upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 24
lower sequence: LOC_Os06g05180.3 (Oryza sativa), 5'ss of exon 9
TACACAGAGGAGCAGGAGGAACAGAATGGAGAGGAAGGAAGCCAAGAGGAGGCAGTTGTAGTGGATGCAGATTCTACAGATGGTGCAGTA--CTCGTTAATGgtaacgaggctgacgaagagtggggtacgaataatgaaggagccccgtcagcctaaaagcaattggttggggtggtgtgaaaatcaaaattttgtctctg-------
        ||   ||  ||    |||  | | || | ||| | | || |   |      ||   |     ||| |   |   ||| |  |  |    |  ||    ||  | |     ||  | |    | ||| ||      |      |   |||  | |    | ||  |     || ||  | |    ||||    |        
-------TGGGAAAGAGGGTGAGGAACAGTGGGGTACGAA-CAATGAAGGAACTTCGTCAGCCTAAAAGAATTGTTTGGCAAGTGTAAAAACCCAAATTTTGTCTGCGgtgattcactagctttgcccccaaattataggactgttgaacctttctagta-cttcagtttttgaaaaagtaaatctgacccctttggaattatagacca

upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 24
lower sequence: AT3G15980.4 (Arabidopsis thaliana), 5'ss of exon 24
TACACAGAGGAGCAGGAGGAACAGAATGGAGAGGAAGGAAGCCAAGAGGAGGCAGTTGTAGTGGATGCAGATTCTACAGATGGTGCAGTACTCGTTAATGgtaacgaggctgacgaagagtggggtacgaataatgaaggagccccgtcagcctaa-aagcaa-ttggttgggg--tggtgtgaaa--atcaaaattttgtctctg------------------
                     ||  | | ||| ||||  |   |||| |||| ||||||   ||||||||| ||||| || ||||| ||||| |||||||| |  |||| ||| ||||||||||||||||||||  |||||  ||| ||||||||| |||||| |  ||   ||     |||  ||   || ||||||||||||||                  
---------------------CAACAGGAAGAAGAAGTGAATGAAGAAGAGGGAGTTGT---GGATGCAGACTCTACGGACGGTGCTGTACTTGTTAATGGAAGTGAGGGTGAGGAAGAGTGGGgtacgaataacaaaggaaacccatcagcctaataagcaagtcagtccaggatcaatgttgaatagtcgaaattttgtctctggtgattaaattgaaacct

upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 24
lower sequence: AT1G79990.5 (Arabidopsis thaliana), 5'ss of exon 24
--TACACAGAGGAGCAGGAGGAACAGAATGGAGAGGAAGGAAGCCAAGAGGAGGCAGTTGTAGTGGATGCAGATTCTACAGATGGTGCAGTACTCGTTAATGgtaacgaggctgacgaagagtggggtacgaataatgaaggagccccgtcagcctaaaagcaattggttggggtggtgtgaaaatcaaaattttgtctctg--
  |   |||      || ||  |  | |   ||  ||| |  |  |||| ||||| ||||| ||||| || || ||||| |||||||| || || ||||||||||||||| |||| ||| ||||||||| || || ||||||| || | ||||||| | |||| || || |   |    |||  || || || | |   |    
GATCGTCAGGAAGAGAGTAGTGATGGGAGACAGCAGAATGTGG--AAGAAGAGGCTGTTGTGGTGGACGCTGACTCTACGGATGGTGCTGTGCTAGTTAATGgtaacgagtctgaagaacagtggggtaagattagtgaaggaaccgcatcagccttatagca-tttgtggttatcaattgattat-aagatgtcgctgcacca

upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 24
lower sequence: AT3G15980.1 (Arabidopsis thaliana), 5'ss of exon 24
TACACAGAGGAGCAGGAGGAACAGAATGGAGAGGAAGGAAGCCAAGAGGAGGCAGTTGTAGTGGATGCAGATTCTACAGATGGTGCAGTACTCGTTAATGgtaacgaggctgacgaagagtggggtacgaataatgaaggagccccgtcagcctaa-aagcaa-ttggttgggg--tggtgtgaaa--atcaaaattttgtctctg---
      |  ||  | ||||||||  | | ||| ||||  |   |||| |||| ||||||   ||||||||| ||||| || ||||| ||||| |||||||| |  |||| ||| ||||||||||||||||||||  |||||  ||| ||||||||| |||||| |  ||   ||     |||  ||   || ||||||||||||||   
------GGAGATGAAGAGGAACAACAGGAAGAAGAAGTGAATGAAGAAGAGGGAGTTGT---GGATGCAGACTCTACGGACGGTGCTGTACTTGTTAATGGAAGTGAGGgtgaggaagagtggggtacgaataacaaaggaaacccatcagcctaataagcaagtcagtccaggatcaatgttgaatagtcgaaattttgtctctggtg

upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 24
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 24
TACACAGAGGAGCAGGAGGAACAGAATGGAGA-GGAAGGAAGCCAAGAGGA-GGCAGTTGTAGTGGATGCAGATTCTACAGATGGTGCAGTACTCGTTAATGgtaacgaggctgacgaagagtggggtacgaataatgaaggagccccgtcagcctaaaagcaattggttggggtggtgtgaaaatcaaaattttgtctctg---
 |  | || ||  ||  ||    ||||   || ||||      ||     |  |||  |   ||  | ||  ||  |  | |   || |    | ||   |||| |  |   |||      |    |  ||  |  | |   | |    || |   |   |    |||||         || |  ||| |        |  |   
-AGGCTGACGAAGAGTGGGGTACGAATAATGAAGGAAACCCATCAGCCTAATAGCAAGT-CGGTCAAGGCCAATGTTGAAAAGTCTGAAAATTTTGTCTCTGgtgattaatttgattccccgaaaagc-cgccttctaac--atctttttccgttgatgtgtgtctggtttcaagtcattgcatttcatagcaacccttaggaac

upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 24
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 28
TACACAGAGGAGCAGGAGGAACAGAATGGAGAGGAAGGAAGCCAAGAGGAGGCAGTTGTAGTGGATGCAGATTCTACAGATGGTGCAGTACTCGTTAATGgtaacgaggctgacgaagagtggggtacgaataatgaaggagccccgtcagcctaaaagcaattggttggggtggtgtgaaaatcaaaattttgtctctg--------------------------
                       | |   ||  ||| |  |  |||| ||||| ||||| ||||| || || ||||| |||||||| || || ||||||||||||||| |||| ||| ||||||||| || || ||||||| || | ||||||| | |||| || || |   |    |||  || || || | |   |                            
----------------------GGGAGACAGCAGAATGTGG--AAGAAGAGGCTGTTGTGGTGGACGCTGACTCTACGGATGGTGCTGTGCTAGTTAATGGTAACGAGTCTGAAGAACAGTGGGgtaagattagtgaaggaaccgcatcagccttatagca-tttgtggttatcaattgattat-aagatgtcgctgcaccaaaatatccttttgccatctgcaca

upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 24
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 25
TACACAGAGGAGCAGGAGGAACAGAATGGAGAGGAAGGAAGCCAAGAGGAGGCAGTTGTAGTGGATGCAGATTCTACAGATGGTGCAGTACTCGTTAATGgtaacgaggctgacgaagagtggggtacgaataatgaaggagccccgtcagcctaaaag-caattggttggggtggtgtgaaaatcaaaattttgtctctg-----------------------------------------------------------------
                                                                  || |||||||| ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||| | || || ||||||||| ||||||||||||   ||||||||||| ||||||||||||||                                                                 
------------------------------------------------------------------GCTGATTCTACTGATGGTGCAGTACTCGTTAATGGTAACGAGGCTGAAGAAGAGTGGGGTACGAATAATGAAGGAACTCCATCGGCCTAAAAGGCAATTGgttgggccagtgtgaaaatccaaattttgtctctggtgattaattgattttctttgaagtgccatctctgactcgcagtttgagtttttgtccttgctac

upper sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 24
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 24
TACACAGAGGAGCAGGAGGAACAGAATGGAGAGGAAGGAAGCCAAGAGGAGGCAGTTGTAGTGGATGCAGATTCTACAGATGGTGCAGTACTCGTTAATGgtaacgaggctgacgaagagtggggtacgaataatgaaggagccccgtcagcctaaaagcaattggttggg-gtggtgtgaaaatcaaaattttgtctctg----------------------------------------------------------------------------
                                                                          | ||||  |     |||| ||||||||||| |||| ||| |||||| ||||| | |||||||||||| |  |  | |  | ||   ||||| |||||  |  |||||  ||| ||||||||| ||||                                                                            
--------------------------------------------------------------------------TCCAGACAG---GATACTTGTTAATGGTAATGAGGGTGAAGAAGAGCGGGGTGCAAATAATGAAGGAACTTCTACTGATTGAAGTTAATTGTTTGGGCATACTgtgagtatccaaattttgtttctggtgattagttaatttgctttaaatgcttctccaactccctttttaacatatactgctgctgctgctgctactatga

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACACAGAGGAGCAGGAGGAACAGAATGGAGAGGAAGGAAGCCAAGAGGAGGCAGTTGTAGTGGATGCAGATTCTACAGATGGTGCAGTACTCGTTAATGgtaacgaggctgacgaagagtggggtacgaataatgaaggagccccgtcagcctaaaagcaattggttggggtggtgtgaaaatcaaaattttgtctctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggtgg