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'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgctatcaggattcatgtacatttaatcaattctcagtgtataagttcctttctttgacttaataattcttatgtttattactttatcaaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT

Basic information

species Zea mays
transcript GRMZM2G057576_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 11
-------cctgctatcaggattcatgtacatttaatcaattctcagtgtataagttcctttctttgacttaataattcttatgtttattactttatcaaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT
         | || ||  |  |   |    |  ||  ||| || | ||  || | || | |  ||||||||    || ||   ||   | |||||    || |||||||||||||||| |||||||||||||| || ||||||||||||||||||||||||||||||||||| |||||||||||||| |  ||||||||||||||||
attttcatttactttcctgtgttgggactgtacaactaat-cttaatgcttatgctcttctgcttgacttagc--tttttcgtttctgtgcttta----aaatgcagAGTGTTCCTGTTCAAGCTGGGCAAACGCCTCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGGGGGAAGCTCAATGCTTACGAGTCTCTTGAGCTAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 11
-------cctgctatcaggattcatgtacatttaatcaattctcagtgtataagttcctttctttgacttaataattcttatgtttattactttatcaaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT
         | || ||  |  |   |    |  ||  ||| || | ||  || | || | |  ||||||||    || |  | | | |   ||||     | |||||||||||||||| |||||||||||||| || ||||||||||||||||||||||||||||||||||| |||||||||||||| |  ||||||||||||||||
attttcatttactttcctgtgttgggactgtacaactaat-cttaatgcttatgctcttctgcttgacttagct-ttttcgtttctgtgctttta-----aatgcagAGTGTTCCTGTTCAAGCTGGGCAAACGCCTCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGGGGGAAGCTCAATGCTTACGAGTCTCTTGAGCTAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 11
cctgctatcaggattcatgtacatttaatcaat-tctcagtgtataa-gttcctttctttgacttaataattcttatgtttattactttatcaaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT
     | | |    |   ||     |||| | |  |||| | |||     |    ||| |  || ||   |||||  |||   |   |||      || |||||||| |||||||||||||||||||| || ||  | ||||| |||||||| ||  || ||||    || || |||||||| |||||||| || || || |
tacaatttaaaaccttgggtgtgcctaatgactacctcattatatgttaatatgctctctatctcaa--gttcttgagttacctttgttaatttgctttcagAGTGTACCTGTGCAAGCTGGGCAAACGCCACCGTTATTGCAATACTTTGGAACTCTGTTAACCATGGGAAAACTCAATGCTTTTGAGTCACTGGAACTGT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 11
----------------------------------------------------cctgctatcaggattcatgtacatttaatcaattctcagtgtataagttcctttctttga---cttaataa----ttcttatgtttattactttatcaaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT
                                                    |||| ||  ||  ||      || ||      |  | | |   |  |    ||| | ||     | ||||     || ||   | |||| ||||||     || |||||||| ||||||||||||||||| || || ||||| |||||||||||||| ||  || ||||  | || || |||||| | | ||||||  | || || |
gtacacttttgtgtttagattttctctgttgtacatgccggtgcttcttgttcctgtta--agtgttttctctcagttgtatggtgtttattaattgtggcgatttatatgggagttcaatatgcttttttttcatctatttctttattttcttttcagAGTGTACCTGTGCAAGCTGGGCAGACGCCACCACTGTTGCAGTACTTTGGTACTCTGTTAACCAGGGGAAAACTCAATTCTTATGAGTCATTGGAACTGT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 11
--------------------------------------------------------------------------------cctgctatcaggattcatgtacatttaatcaattctcagtgtataagttc---ctttctttgacttaataa--ttcttatgttta-------ttactttatcaaa-attgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT
                                                                                | || | | |||  | | | | |   ||  ||||   | ||| || |||    |||| | |   | ||| |   | | ||| |||       | | | | |   |  | |||||||||||||||||||||||||||||| || ||||| |||||||| ||||| ||| | |||||  |||| ||||| ||||||||||||||  | ||  | |
gttttgtatataagatacagccatcaaatattttgttcgtgctctttcatcaacaaatttaacctagacaatcatctttgcttgttttgagggataaaggata--aaaggaatttgaactgtttaggtttgttctttttcttggtcaattaggctatcatggttaaagtgtgtcaatctgttttatgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCACTATTGCAGTATTTTGGAACACTTCTAACAAGAGGAAAGCTGAATGCCTTTGAGTCATTGGAATTGT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 10
---------------------------------------------------------------------cctgctatcaggattcatgtacatttaatcaattctca---gtgtataagttcctttctttgacttaataattcttatgtttattactttatcaaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT
                                                                     | |  |     | |   | | ||||    |||||   |   | ||  ||  | |||| |||   |   || |||||   ||  ||  |  ||     || |||||||| ||||||||||||||||| ||||| ||||| || ||||||||||| ||  || ||||  | || || |||||| | | ||||||  | ||  | |
gtacactttcgtatctagattttctctgttgtacatgccagtgcttcttgctcctgttaagtgttttctcttagttgtgtggtgtttattcattgtggcaatttatatgggagttcaatatgcttttttttcatc--tagttcttgatttcttttatcaattt--ttttcagAGTGTACCTGTGCAAGCTGGGCAGACACCACCACTGTTACAGTACTTTGGTACTCTGTTAACCAGGGGAAAACTCAATTCTTATGAGTCATTGGAATTGT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 11
------------------------------------------------------cctgctatcaggattcatgtacatttaatcaattctcagtgtataagt-----tcctttctttgacttaataattcttatgttta--------ttactttatcaaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT
                                                       |    |    ||||||| | |   |  |  | | |  |  | || ||      | ||| ||||    | || || | |||||||        |||  |  |  |  | |||||||||||||||||||| ||||||||| || ||  | |||||||| ||||| ||| |  ||||  | || ||| | ||||||||||| ||  | ||  | |
gtttcttgataagatgttgctatctgggaattttctcttgcttttttagctacttcattcacagagattcattttctggttgtttactgtttgcctttaggtgatgtccttttgtttggtcaattagttataatgtttaaaatgccattatctgctttatgtggcagAGTGTTCCTGTGCAAGTTGGGCAAACTCCTCCTTTGTTGCAGTATTTTGGAACACTTTTAACAAGGGGAAAGTTGAATGCCTTTGAATCATTAGAATTGT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 11
-----------------------------------------------------cctgctatcaggattcatgtacatttaatcaattctcagtgtataagttccttt-ctttgacttaataattcttatgtttattactttatcaaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT
                                                     |     ||     ||   ||     |||| | | |    |  ||| |||  | | || |   |    | |||||  |||   |   ||       || |||||||| ||||||||||||||||||||||| || || ||||| |||||||| ||  || ||||    || || || ||||| |||||||| || || || |
gtatttacgcatcacacatactgatccattcatatttcttggtcttggtaagtcaatgcattcaatttagggtgtgcctaatgactaccacattaatatgttaatatgctgtctatctcaagttcttgagttgcctttgttcatttgctttcagAGTGTACCTGTGCAAGCTGGGCAAACACCACCGCTGTTGCAATACTTTGGAACTCTGTTAACCATGGGAAAACTGAATGCTTTTGAGTCACTGGAACTTT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 11
----------------------------------------------------------------------------cctgctatcag-gattcatgtacatttaatcaattctcagtgt------ataagttcctttctttgacttaataa-ttcttatgtttattactttatca--------aaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT
                                                                              ||     |  |||  ||  |   | ||  | ||   | |||       |  |||| |||  |||    | ||   | | |||||||     | |  |        |  | |||||||||||||||||||||||||||||| || ||||| |||||||| ||||| ||| | |||||  |||| ||||| ||||||||||||||  | ||  | |
gttttgtatataagatatagccatcaaatattttagttgtgctctttcatcaacaaatttaacctagacaatcatctttgtggagaatgatggataaaggataaaagagtttgaaatgtttttaggtttgttctttttcttggtcaattaggctgtcatgtttaaagtgtcacgatctgttttatgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCACTATTGCAGTATTTTGGAACACTTCTAACAAGAGGAAAGCTGAATGCCTTTGAGTCATTGGAATTGT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 11
-----------------------------------------------------cctgctatcag-gattcatgtacatttaatcaattctcagtgtataagt-----tcctttctttgacttaataattcttatgttta--------ttactttatcaaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT
                                                       |  |  ||| ||||||| | |   |  |  | | |  |  | || ||      | ||| ||||    | || || | |||||||        |||  |  |  |  | |||||||||||||||||||||||||||||| || || || |||||||| ||||| ||| |  ||||  | || ||||| ||||||||||| ||  | ||  |||
gtttcttgataagatgttgctatctgagaattgtctcttgcttttttagccactttattcacagagattcattttctggttgtttactgtttgcctttaggtggtgtccttttgtttggtcaattagttataatgtttaaaatgccattatctgctttacgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCTCTGTTGCAGTATTTTGGAACACTTTTAACAAGGGGAAAGCTGAATGCCTTTGAATCATTAGAATTAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 11
--cctgctatcaggattcatgtacatttaatcaattctcagtgtataagttcctttctttgacttaataattcttatgtttattactttatcaaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT
       ||| || ||| | |    |   |||| || |   | | ||   |   ||     |    |  ||| | || | | ||  || ||     ||||||||||| ||||||||| |||| || ||||| || || |||||||||||||| ||  || ||||  |||| || |||||||| || || || || ||  | |
gatgctttatgagaattgaagagtttgctatcatttttacttatttataataaattgggaaaacacaagattgtcatctgtttttgttcattt--tttgcagAGTGTCCCTGTGCAATCTGGACAGACACCACCTCTGTTGCAGTACTTTGGTACTCTGTTAACCAGAGGAAAACTCAATGCTTTCGAATCACTGGAATTGT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 11
cctgctatcaggattcatgtacatttaatcaattctcagtgtataagttcctttctttgacttaataattcttatgtttattactt-tatcaaaatt--gcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT
 || |  | |   ||  | |   |||||  ||   |        |  ||    |     |  |  |||    | ||| |  | ||  | || || ||  ||||||||||||| ||||| ||||||| || || ||  |  | ||||||||||| ||| | |||||| |||| ||||||||||| ||||||||  | ||  |||
-cttccttta--ttttttatttttttaaaaaaccattccctggaattttggggtgggaaagatgctaaccactttgtcttcttctggtgtctaatttttgcagAGTGTTCCTATGCAATCTGGGCAGACTCCACCTTTGCTACAGTACTTTGGAACACTTCTAACTAGAGGAAAGCTCAATGCATTTGAGTCATTGGAATTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttcctttctttgacttaataattcttatgtttattactttatcaaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT
              acttaat  putative branch site (score: 4)
              acttaataattcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctgctatcaggattcatgtacatttaatcaattctcagtgtataagttcctttctttgacttaataattcttatgtttattactttatcaaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA