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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgattttcttaacggtcactgatgatatgcctatgacataataagttgtagcttactcattgatttgtgtcctgtatattagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA

Basic information

species Zea mays
transcript GRMZM2G157621_T02
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
-gttagtgattttcttaacggtcactgatgatatgccta--tgacataataa-gttgtagcttactcattgatttgtgtcctgtatatt---------agGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA
 || | | | | | ||     |  |  |||||    |    |  ||| ||   | | || | |  | | |   ||   | || |  |||         ||||||||||||||||||||||| | ||||| |||||||||||||| || ||||||||||||||||||||||||||||| || ||||||||||| || ||||
tgtgaatcactcttttttatattgcctatgattcagcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA

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

upper sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
gttagtgattttcttaacggtcactgatgatatgcctatgacataa-taagttgtagcttactcattgatt-tgtgtcctgtatattagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA
|| ||   |||   |||  ||   |  |  | |  | ||   | |  | |    ||  | | | |    |  | || | | |    ||||||||| ||||| |||| ||  | || ||||| ||||| |||||||||||||| |||||||||||||| || |||||||| ||||||||  |  | ||||
gtaagccttttgtataaatgttcttagtt-tgtatcaattcaacagctgaaaaataaatcagtgaaaactagtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA

upper sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
gttagtgattttcttaacggtcactgatgatatgcctatg-acataataagttgtagcttactcattgatt-tgtgtcctgtatattagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA
|| ||   ||| |  ||  ||   | ||  | |  | ||  |  |  |      ||  | | | |    || | || | | |    ||||||||| ||||| |||| ||  | || ||||| ||||| |||||||||||||| |||||||||||||| || |||||||||||||||||  |  | ||||
gtaagccttttgcacaaatgtttttaatt-tgtatcaattcatctgctgcaaaataaatcagttaaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA

upper sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 19
gttagtgattttcttaacggtcactgatgatatgcctatgacataataagttgtagcttactcattgatttgtgtcctgtatattagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA
    || |   | |||||      | | | |||   | ||   | ||   ||| |  | |||       ||     || | | | |||||||  ||||| ||||| |  | || || ||||| || |||||||||||||| |||||||||||||| || |||||||| ||||||||  |  | || |
----gtaagccttttaac-----ttaagggtattgttttgtattgattcattggatgtaact-------ttactagctttgtttcagGTTGACAGCATGTTGGGTCGTAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACGA

upper sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 22
-------gttagtgattttcttaacggtcactgatgatatgc-ctatga-cataataagttgtagcttact-cattgatttgt---gtcctgtatattagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA
        | |    ||   |   |  |   | ||||||    ||||||   |  | ||||  |  |  ||   |||||||||   | |   | |   |||||||| | ||||| || |||||||| || ||  | || |||||||| ||||| || |||||||||||||||||||| || |||||||||||  | ||||
tgaagacctaaacatttaaatctccaattttttatgatagctactatgaattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTAGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA

upper sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
gttagtgattttcttaacggtcactgatgatatgcctatgacataataagttgtagcttactcattgatttgtgtcctgtatattagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA
    || |   | ||||      |  | | |||   | ||   || | | |  | |  ||    || | | |    || | | | |||||||  ||||| ||||| |  | || || ||||| || |||||||||||||| |||||||||||||| || |||||||| ||||||||  |  | || |
----gtaagccttttaa------ccaagggtat---tgtgttgtattgattcattgaatataactttactag----ctttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA

upper sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 19
----------------gttagtgattttctt-aacggtcactgatgatatgcctatgacataataagttgtagcttactcattgatttgtgtcctgtatattagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA
                  ||||| |||||||     |   ||   ||||| | |       ||| |  |||   | | |  ||   ||||| | |   |   |||||||| | ||| | || |||||||| ||||| || ||||||||||| ||||| || ||||| ||||| || ||||| || ||||||||| | || ||||
aaatgagcattcagaatctagtgtttttctttggtagcttctacagatattcttgct-ttcaattatctgtgtttgatttgtt---ttgtgacattggtggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAACATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGAGAACAA

upper sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
lower sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
---------gttagt-gattttcttaacggtcactgatgatatgcctatgaca----taataagttgtagcttactcattgatttgtgtcctgtatat-tagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA
         |||  | ||  ||   ||| | | || || |  ||  ||| |||       |   ||   |  ||    ||||   |  ||     ||| ||||||||| |||||||||| ||||||||||||||||| |||||||| || ||||| |||||||| || || || ||| | |||||||| ||  |  | ||||
atgaggtatgttgctagacgttaagaacag-ctctcat-acctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA

upper sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
----gttagt-gattttcttaacggtcactgatgatatgcctatgaca----taataagttgtagcttactcattgatttgtgtcctgtatat-tagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA
    |||  | ||  ||   ||| | | || || |  ||  ||| |||       |   ||   |  ||    ||||   |  ||     ||| ||||||||| |||||||||| ||||||||||||||||| |||||||| || ||||| |||||||| || || || ||| | |||||||| ||  |  | ||||
gtatgttgctagacgttaagaacag-ctctcat-acctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA

upper sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 22
-----gttagtgattttcttaa-cggtcactgatgatat--gcctatgacataataagttgtagcttactcattgatttgtgtcctgtata----------ttagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA
      ||   ||| ||   || || || ||| |        ||| |||    |    || ||  |   |  | ||| ||     |||  |          | |||||||| ||||| ||||||||||||| ||||||||||||||||| || ||||| |||||||| || ||||| ||||| |||||||||||| | || ||||
gtatgtttgaagatattaaaaagcgttctctgttctctcccacctttgaagccagtctttttatgtactttctcgatctgatgattgtggaaaatcattattcagGTTGATAGCATGTTGGGTAGACGTGAAAATCCAGGGGAACATGAAGCTATGCGTAAGATGAAGAACGAGTTCATGGTAAACTGGGATGGTTTAAGAACAA

upper sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 22
----------------------------------------------------------------------------------------gttagt-gattttcttaacg-gtca--ctgatgatatgcctatgacataataagttgt----agcttactcattgatttgtgtcctgtatattagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA
                                                                                          |  |  ||  | ||||   | ||  |||||  |  |  | |  | |  |    |||    |  ||  |  || | ||   |    | | | |||||||  ||||| | || |||||||| |||||||| |||||||| || ||| | || ||||| |||||||| ||||||||||||||||| ||  | ||||
gtaagttgaataaatctttaaattcatccacaacttttgctataatgttcctcactctttttatgggtccatggatttagtgacggtaactgttcaatccttttaattcgccattctgatctttagtttctttcttcttttcctgttaaaaaatttattgttaacttagatttattgtttcagGTTGACAGCATGTTAGGGAGACGTGAAAATCCAGGAGAACATGAAGCTATGAGGAAAATGAAGAATGAGTTCATGGTGAACTGGGATGGCCTACGTACAA

upper sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 23
gttagtgattttcttaacggtcactgatgatatgcctatgacataataagttgtagcttactcattgatttgtgtcctgtatattagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA
    ||||  ||| ||    | |||  |  | ||  |||    |  |   ||      | ||   |   || | |  |   | |||||||||| ||||||||||  |  | ||||||||||||||||||||||||||||| ||||||||||| || |||||||| |||||||||||  |  | ||||
----gtgagcttcata----taactctt--tttgtttatatattgtttgcttcctctctgcttgctatattctttgtttggtcttagGTTGATAGCATGCTGGGCCGGAGGGAGAATCCAGGGGAACATGAGGCCATGCGTAAGATGAAAAACGAATTTATGGTCAACTGGGATGGCTTGCGCACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctatgacataataagttgtagcttactcattgatttgtgtcctgtatattagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA
          ataataagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgattttcttaacggtcactgatgatatgcctatgacataataagttgtagcttactcattgatttgtgtcctgtatattagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG