Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaactttttttttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA

Basic information

species Zea mays
transcript GRMZM2G126453_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 23
gtatgc--aagcacacaagtttact---------ttagtaaccactaccggcacagtatataccaactttttttttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
||||||   ||||     |||   |         ||||| |    |   | ||| ||||  | | |       |   || ||  |||||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| || ||||||||||| ||||||||||| || |||||||
gtatgcttgagcatgtgggttggttttattgtcattagtgatttatttggtcacggtatg-atccatacaaaatgcaacatttggcagGTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAAAACGAATTTATGGTGAATTGGGATGGATTACGCACTA

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

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 19
---------gtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaacttttttt--ttgactttctg------------cagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
          ||| |||    |    ||| |||| ||| |  |||| |  |   |   |  ||| | | | |  |||| || |||            ||||| ||||||||| |||||||  | |||||||| || |||||||| || ||||| || |||||||||||||| ||||| ||||||||||| ||||| || |
ggcttaaacatattcaaatctagtgtttttctttggtagcttctacggatattcttagtttcaattatctgtgtttgatttgctgtgttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
---------gtatgcaagcacaca-agtttactttagtaaccactaccggcacagtatat-accaactttttttttgactttctgca--gGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
          | |  ||     |  |||||   | | |   ||  | | | | | || || |   |    |  | || |||  || |  ||| ||||| ||| | || ||||| |||||||| ||||||||||| || ||||| |||||||| |||||||| ||||| ||||||||||| || ||||| |
gtaagccttttgtataaatgttcttagtttgtatcaat--tcaacagctgaaaaataaatcagtgaaaactagtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
gtatgcaa---gcacacaagttt---actttagtaaccactaccggcacagtatataccaactt---tttttttgactttctgca--gGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
||| ||     ||||| | ||||   | ||   | |   |  | |   ||  ||| | ||  |     || | || |||  || |  ||| ||||| ||| | || ||||| |||||||| ||||||||||| || ||||| |||||||| |||||||| ||||| || |||||||| || ||||| |
gtaagccttttgcacaaatgtttttaatttgtatcaattcatctgctgcaaaataaatcagttaaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 19
gtatgcaagcacacaagtttactt-tagtaaccactaccggcacagtatataccaactttttttttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
    | ||||     |  |||    || |      ||  |   || |  ||   |    |||  | |  ||  | ||||| || || ||| | ||  | || ||||| ||||| |||||||| || ||||| |||||||| |||||||| ||||| ||||||||||| || ||||| |
----gtaagccttttaacttaagggtattgttttgtattgattcattggatgtaa---ctttactagctttgtttcagGTTGACAGCATGTTGGGTCGTAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACGA

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 22
-----------gtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaacttttttt-ttgactttctg------------cagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
             ||  ||   | | | |||  | |  || | ||||         |   |  ||| | | | | |||| ||  ||            ||||| |||||||||||||| ||  | ||||| ||  | |||||||| || ||||| || ||||| ||||| ||||||||||||||||||||  |||| || |
tgaagacctaaacatttaaat-ctccaattttttatgatagctactatgaattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTAGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
gtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaactttttttttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
    | ||||     |    |   || |      ||  |   || |  |||  |    |||  | |  ||  | ||||| || || ||| | ||  |||| ||||| ||||| |||||||| || ||||| |||||||| |||||||| ||||| |||||||||||||| ||||| |
----gtaagccttttaaccaagggtattgtgttgtattgattcattgaatataa---ctttactagctttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 19
------gtatgca-agcacacaagtttactttagtaaccactaccggcac-----------agtatatac---caactttttttttgacttt--ctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
      | || || |    |    ||| |||| ||| |  |||| |  |            | ||| |       | || |||| |||| ||    |||||| ||||||||| |||||||  | |||||||| || || ||||| || ||||| || |||||||||||||| ||||| ||||||||||| ||| | || |
aaatgagcattcagaatctagtgtttttctttggtagcttctacagatattcttgctttcaattatctgtgtttgatttgttttgtgacattggtggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAACATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGAGAACAA

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
------------------------gtat-gcaagcacacaagtttactttagtaaccactaccggcacagtatataccaactttttttttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
                        | |  ||   || ||  ||||| |  |||  |   | |   |  | ||| |    |      |    |  || || |||| ||||| ||||| |||||  | || |||||||| || |||||||| ||||| ||||||||||| ||||| ||| |||| ||||| || || ||||| |
atgaggtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatc--aaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
-------------------gtat-gcaagcacacaagtttactttagtaaccactaccggcacagtatataccaactttttttttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
                   | |  ||   || ||  ||||| |  |||  |   | |   |  | ||| |    |      |    |  || || |||| ||||| ||||| |||||  | || |||||||| || |||||||| ||||| ||||||||||| ||||| ||| |||| ||||| || || ||||| |
gtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatc--aaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 22
----gtatgcaagcac--acaagtttactttagtaaccactaccggcacag------tatataccaactttttt--tttga--------------ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
    || || |   |   | |||  | || |  |  |  | |||     ||      | | ||   ||||| |   | |||              | || | ||||| ||||| ||| | || ||  | |||||||||||||| |||||||| ||||| ||||||||||| || || |||||||| |||||||| ||  | || |
gtatgtttgaagatattaaaaagcgttctctgttctctcccacctttgaagccagtctttttatgtactttctcgatctgatgattgtggaaaatcattattcagGTTGATAGCATGTTGGGTAGACGTGAAAATCCAGGGGAACATGAAGCTATGCGTAAGATGAAGAACGAGTTCATGGTAAACTGGGATGGTTTAAGAACAA

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 22
---------------------------------------------------------------------------------------------------------gtatgcaagcacacaagtttactttagtaaccactaccggc-acagtatataccaactttttttttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
                                                                                                          |  || |         ||   ||   |   |  | || |  | |  || ||        ||   |   ||  | ||||| || || ||| |||| ||  | ||||||||||| || |||||||| ||| | || ||||||||||| || ||||| || ||||||||  | || || |
gtaagttgaataaatctttaaattcatccacaacttttgctataatgttcctcactctttttatgggtccatggatttagtgacggtaactgttcaatccttttaattcgccattctgatctttagtttctttcttcttttcctgttaaaaaatttattgttaacttagatttattgtttcagGTTGACAGCATGTTAGGGAGACGTGAAAATCCAGGAGAACATGAAGCTATGAGGAAAATGAAGAATGAGTTCATGGTGAACTGGGATGGCCTACGTACAA

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 23
gtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaacttt-ttttttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
||  ||   || | || | |  ||   ||   | |    ||    | | | |   || | || ||||  |      |||| ||||| ||||| ||  |||| || ||||||||||| ||||| || ||||| |||||||| || ||||||||||| || |||||||| |||||||| |
gtgagctt-catataactctttttgtttatatattgtttgcttcctctctgcttgctatattctttgtttggtcttagGTTGATAGCATGCTGGGCCGGAGGGAGAATCCAGGGGAACATGAGGCCATGCGTAAGATGAAAAACGAATTTATGGTCAACTGGGATGGCTTGCGCACAA

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|58029637|gb|CX725064.1|CX725064
EST:     TTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG                         GTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
EST: gi|32920203|gb|CF025015.1|CF025015
EST:     GTGTTATATTTATTGATGAG                         GTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
genomic: GTGTTATATTTATTGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
EST: gi|32934898|gb|CF039710.1|CF039710
EST:     TTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG                         GTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
EST: gi|32920665|gb|CF025477.1|CF025477
EST:     TAAAATAGCACCCAGTGTTATATTTATTGATGAG                         GTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
genomic: TAAAATAGCACCCAGTGTTATATTTATTGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagtaaccactaccggcacagtatataccaactttttttttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
                                 ctttttttttgacttt  CT-rich tract
                                  tttttttttgacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaactttttttttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA