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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagattttgctcatattttttttcatttacttgcaataaaaaccatgatgtttcaacctttttttctttattatgttgcctcggcattttctggcaggcagcatggtaatgactaaaattttatcactagcactccattgtcttgattgtgacttcccgtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC

Basic information

species Zea mays
transcript GRMZM2G421857_T04
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 15
gtagattttgctcatattttttttcatttacttgcaataaaaaccatgatgtttcaacctttttttctttattatgttgcctcggcattttctggcaggc---agcatg-gtaatgactaaaattttatcactagcactccattgtcttgattgt-gact-tcccgtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC
                                                                     || || ||     ||  |||||    || ||    ||||  ||||    | |  |||| |   |  |  |   |  | || ||||| |||| | ||     ||||||||||||||||||| || ||||||||||||||||||||||| |||||||||||||| ||| |||||||||||||||||||||||||||||||||||||
---------------------------------------------------------------------tagtacgta----cgttatttttaaacaagctgtggcataagtaagatttgagcttttgttgtt--ctttgtgtgatatttattgttgactctaccccacattcagCTTGTTGGTAAAGACGCACTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAACTTCTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 15
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 16
gtagattttgctcatattttttttcatttacttgcaataaaaaccatgatgtttcaacctttttttctttattatgttgcctcggcattttctggcaggcagcatggtaatgactaaaattttatcactagcactccattgtcttgattgtgacttcccgtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC
                                                                |||  |   |   |     || |  || |     || |||||   ||||      | || |  ||    | | |  |   |  || ||| ||    |   | |||||||| || ||||||||  | || ||| | || || ||||| || ||||| |||||||||||||| ||||| ||| | |||||||||||||| |||||
----------------------------------------------------------------ttcactggaaaactattagggaaaattatta---gctgcatgtccatgatccctttatttttcctctttcacaaaaggtctatttctgatttg--attactgcagCTTGTCGGAAAAGATGCTTTAGCTGAAACAGATAAAATTACTCTAGAGACTGCAAAGCTTTTGAGGGAAGACTATCTTGCACAAAATGCATTTACCCC

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 15
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 15
gtagattttgctcatattttttttcatttacttgcaataaaaaccatgatgtttcaacctttttttctttattatgttgcctcggcattttctggcaggcagcatggtaatgactaaaattttatcactagcactccattgtcttgattgtgacttcccgtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC
                                                                                                                       |      ||| |      ||  ||    |    |||| |  | |   |||||||| || |||||||||||||| ||    || |||||||  || ||||| || ||||| |||||||| ||||||||||| ||||| || ||||    
----------------------------------------------------------------------------------------------------------------------gtacgtgaactggtgagagat--tcaaagtcagtactttc--ttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACGGCCAAGCTCTTGAGAGAGGATTATTTGGCGCAAAACGCTTTCAGTGT

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 15
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 16
gtagattttgctcatattttttttcatttacttgcaataaaaaccatgatgtttcaacctttttttctttattatgttgcctcggcattttctggcaggcagcatggtaatgactaaaattttatcactagcactccattgtcttgattgtgacttcccgtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC
                                                                                                                          || |   | |     |  |  |  |        |    | |   |||||||| || |||||||||||||| ||    || |||||||  || ||||| || ||||| |||||||| ||||||||||| ||||| || ||||    
-------------------------------------------------------------------------------------------------------------------------gta-cgtgaactggtgagagattcaaagtcagtattttcttttcacagCTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACGGCCAAGCTCTTGAGAGAGGATTATTTGGCGCAAAACGCTTTCAGTGT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|32850183|gb|CD989864.1|CD989864
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGACGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|32921243|gb|CF026055.1|CF026055
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|67026160|gb|CO454909.1|CO454909
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTCGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|32845901|gb|CD985582.1|CD985582
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGACGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|6637071|gb|AW261343.1|AW261343
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGCTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|24774168|gb|CA409422.1|CA409422
EST:     AAGCACGTGAGG-GTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|8368089|gb|BE051034.1|BE051034
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|32921648|gb|CF026460.1|CF026460
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|211529162|gb|FL123428.1|FL123428
EST:     AGCACGTGAGGKGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGVCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGAC
genomic: AGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTG-CAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGAC
EST: gi|211529164|gb|FL123430.1|FL123430
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTA
EST: gi|6020503|gb|AW065431.1|AW065431
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|32849884|gb|CD989565.1|CD989565
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGACGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|211538183|gb|FL123481.1|FL123481
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGYGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|32846431|gb|CD986112.1|CD986112
EST:     AAGCACGTCAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGACGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|32846734|gb|CD986415.1|CD986415
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGACGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|8368090|gb|BE051035.1|BE051035
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|8665370|gb|BE186186.1|BE186186
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTCGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|40334940|gb|CK369010.1|CK369010
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGACGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|22542087|gb|BU092525.1|BU092525
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|6227177|gb|AW155706.1|AW155706
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|32921742|gb|CF026554.1|CF026554
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|32920116|gb|CF024928.1|CF024928
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGCCGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|32921546|gb|CF026358.1|CF026358
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
EST: gi|60352649|gb|DN219622.1|DN219622
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaattttatcactagcactccattgtcttgattgtgacttcccgtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC
                                       cttcccgt  CT-rich tract
     ttttatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagattttgctcatattttttttcatttacttgcaataaaaaccatgatgtttcaacctttttttctttattatgttgcctcggcattttctggcaggcagcatggtaatgactaaaattttatcactagcactccattgtcttgattgtgacttcccgtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACGCTGGAGACAGCAAAGCTTTTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG