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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaagaactaaacatttaaatctcatattttttatggtagctactatggattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA

Basic information

species Glycine max
transcript GLYMA02G17410.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
--tgaagaactaaacatttaaatctcatattttttatggtagctactatggattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
  ||||  |||     |||| ||  | |||  || | |   ||||  |||  |||  ||  |     | |  |   |   ||   |       || | | |||||||| | ||||| || ||| | || |||||  | || ||||| |||||||| || |||||||||||||||||||||||||||||||||||| | ||||
tgtgaatcactcttt-tttatattgcctatgattca-gcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 23
-tgaagaactaaacatttaaatctcatattttttatggtagctactatggattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
 | |  || |    ||| |    ||| |     | |   |  | |    ||| ||     | |   ||||||   |    ||||        ||||   |||||||| | ||| | || || |||||||||||| | || ||||| || ||||| ||||||||||||||||||||||| || |||||||||||  | ||||
gtaagtaaattgtaattgatcaatcacaacgcctttctgaattccctgtgatgtttgctttctagtttatcttcttcatcttgt-------gttgta-tagGTTGATGGCATGTTGGGTAGGCGTGAAAACCCTGGAGAACATGAAGCAATGCGTAAAATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTAAGAACAA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 23
tgaagaactaaacatttaaatctcatattttttatggtagctactatggattttcttagtttca--attatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
           |   || |   |     ||  | |  | |  | ||  |||||  || ||  |   || |||  |    | |    |   || |||  |||||||||||||||||| || ||  | || || ||  | |||||||| || ||||| || |||||||| || |||||||| |||||||||||  | || || |
---------gtatgcttgagcatgtgggttggttttattgtcattagtgatttatttggtcacggtatgatccatacaaaat----gcaacatttg--gcagGTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAAAACGAATTTATGGTGAATTGGGATGGATTACGCACTA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
tgaagaactaaacatttaaatctcatattttttatggtagctactatggattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
        ||   ||||   |  |   |   | ||| ||  | |    ||  |  | ||||  |  |  ||   |||||||||   | |   | |   |||||||| | ||||| || |||||||| || ||  | || |||||||| ||||| || |||||||||||||||||||| || |||||||||||  | ||||
------gttagtgattttcttaacg-gtcactgatgata--tgcctatgacataataagttgtagcttact-cattgatttgt---gtcctgtatattagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
-----------------------tgaagaactaaacatttaaatctcatattttttatggtagc-tactat--ggattttcttagtttca-atta---------tctgtgttgatttgttgtggcaat-------tgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
                         | |||| |    | |  || | || | |   | |  | |  | |||  | | ||| | | |  |  ||||         | | || | |||| |  ||    |       | |   |||||||| | ||||| || || || || |||||| | || ||||| || ||||| || |||||||||||||||||||| || |||||||||||| | ||||
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 14
tgaagaactaaacatttaaatctcatattttttatggtagctactatggattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
                         |||       |  || |   ||   |   |   |||   |   | |      | |   | || |  ||   |||||| ||||||||||| || ||  | ||||| ||  | |||||||| || ||||| || ||||| ||||| |||||||||||||||||||| ||||| || |
------------------------gtatgcaagcagacaggttacattagtaaacactgttggtacagtgtacaccaactgtctttgac--tttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGACTGCGCACTA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
tgaagaactaaacatttaaatctcatattttttatggtagctactatgg--attttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
  |   |||  || | |    ||   |   |  |  || |  |   |||           ||   |    |   || | |||| |  || |  |  |   |||||||| | ||| | || || || || |||||| | || ||||| || ||||| || |||||||||||||||||||| || |||||||||||| | ||||
--acttactccacctctgggactttgaacgtccaatgtggagagcctggcagccgaggaggtgggaggctttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------------------tgaagaactaa-acatttaaatctcatattttttatggtagctactatggattttct-tagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
                                                                                                 |  |   |||    |     |   ||   | | | | ||   |  | |  ||  | | | | | ||    |   || | |||| |  || |  |  |   |||||||| | ||| | || || || || |||||  | || ||||| || ||||| || |||||||||||||||||||| || |||||||||||| | ||||
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagt--ttgttgtcaatcctatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G370521_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------tgaagaac-taaacatttaaatctcatattttttatggtag----ctactatggattttcttagtt-tcaatta----------------tctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
                                                                           ||     | | |||||||     | || | |  | |   ||    | || ||  || |  || ||| |||||                  |   || | |||| |  || |  |  |   |||||||| | ||| | || || || || |||||| | || ||||| || ||||| || |||||||||||||||||||| || |||||||||||| | ||||
gtacgtactggtctaattaaaggtgcatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatatgtagtttgttgtcaatcccatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G435582_T01 (Zea mays), 3'ss of exon 3
tgaagaactaaacatttaaat-ctcatattttttatggtagctactatggattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
             ||  ||   | ||  |||  | | |||   ||||  |      |   |  ||| | |||       ||| || || |  ||   |||||| ||||||||||| || ||  | ||||| ||  | |||||||| || ||||| || ||||| ||||| ||||||||||||||||||||  |||  || |
-----------gtatgcaagcacacaagtttactttagtaatcactaccggcacagtatataccaact-tct-------ttttttttgac--tttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCACACTA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
tgaagaactaaacatttaaat-ctcatattttttatggtagctactatggattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
             ||  ||   | ||  |||  | | ||| | ||||  |      |   |  ||| | | | | |||| ||  ||            ||||| ||||||||||| || ||  | ||||| ||  | |||||||| || ||||| || ||||| ||||| ||||||||||||||||||||  |||| || |
-----------gtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaacttttttt-ttgactttctg------------cagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G438355_T01 (Zea mays), 3'ss of exon 2
-------------------------------------tgaagaactaaac---atttaaatctcatattttttatggtagctactatggattttct-tagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
                                     |    |  | ||    | |   |   ||   | ||| | ||   |  | |  |||   | | | | ||    |   || | |||| |  || |     |   |||||||| | ||||| || || |  || |||||||| || ||||| || ||||| || ||||||||||||| |||||| || |||||||||||  | | ||
gtaagttatagtagtgttgtgattcatgtacattttctacttatttcaattgtactaggacaccaccatatttgtagt--ttgttgtcaattccatattgatgcatactttcttgctcatttatcatgccctagtttttagGTTGATGGCATGCTGGGAAGGCAGGAGAACCCTAGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTCTATGGTGAACTGGGATGGTCTCAGAAGAA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G417650_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------------------tgaagaactaa-acatttaaatctcatattttttatggtagctactatggattttct-tagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
                                                                                                 |  |   |||    |     |   ||   | | | | ||   |  | |  ||    | | | | ||    |   || | |||| |  || |  |  |   |||||||| | ||| | || || || || |||||| | || ||||| || ||||| || |||||||||||||||||||| || |||||||||||  | ||||
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagcattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagt--ttgttgtcaatcccatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTAAGAACAA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G482077_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------------------tgaagaactaa-acatttaaatctcatattttttatggtagctactatggattttct-tagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
                                                                                                 |  |   |||    |     |   ||   | | | | ||   |  | |  ||    | | | | ||    |   || | |||| || || |  |  |   |||||||| | ||| | || || || || |||||| | || ||||| || ||||| || |||||||||||||||||||| || ||||||| |||| | ||||
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagt--ttgttgtcaatcccatattgatgcatactttcctgctcatttattctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGATCTGAGAACAA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G354532_T01 (Zea mays), 3'ss of exon 2
tgaagaactaaacatttaaat-ctcatattttttatggtagctactatggattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
             ||  ||   | ||  |||  | | ||| | ||||  |      |   |  ||| |   | | |||| ||  ||             |||| ||||||||||| || ||  | ||||| ||  | |||||||| || ||||  || ||||| ||||| ||||||||||||||||||||  |||| || |
-----------gtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaacttctttttttgactttctgg------------agGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCACAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 22
tgaagaactaaacat-ttaaatctcatattttttatggtagctactatggattt--tcttagtttcaattatctgtgttgatttgttgtggcaa-ttgtgg--cagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
 | |    | || || |||||   | |  | | |    |  |  || || |     ||||  | |  | | |||   |    |  |||||| || |  |    ||||||||||| ||| | || ||||||||||| ||  | || ||||| |||||||| || ||||| || ||||| |||||||| ||||||||| |  | ||||
-gtatgtttgaagatattaaaaagcgttctctgttctctcccacctttgaagccagtctttttatgtactttctcgatctgatgattgtggaaaatcattattcagGTTGATAGCATGTTGGGTAGACGTGAAAATCCAGGGGAACATGAAGCTATGCGTAAGATGAAGAACGAGTTCATGGTAAACTGGGATGGTTTAAGAACAA

upper sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 22
--------------------------------------------------------------------------------------tgaagaactaaacatttaaatctcatattttttatggtagctactatggattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
                                                                                      | |      || | ||| |||     ||| |      ||| | || |    |||    |||  ||   |   |||| | ||    |    |||||  |||||||| || ||| | |||||||||||||| ||  | || ||||| |||||| | |||||||| |||||||| ||||| || |||||||| || |||||||
gtaagttgaataaatctttaaattcatccacaacttttgctataatgttcctcactctttttatgggtccatggatttagtgacggtaactgttcaatccttttaattcgccattctgatctttagtttctttcttcttttcctgttaaaaaatttattgttaacttagattt---attgtttcagGTTGACAGCATGTTAGGGAGACGTGAAAATCCAGGAGAACATGAAGCTATGAGGAAAATGAAGAATGAGTTCATGGTGAACTGGGATGGCCTACGTACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA
                           tgttgat  putative branch site (score: 4)
          ttagtttcaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaagaactaaacatttaaatctcatattttttatggtagctactatggattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA

- - - -ctaaaca
- - - - - - - - - - - - - - - - - - - -gctacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atctgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgtgg