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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCCTGGAAGGCAAAATGACCGTAAAACTCTTCTTGGGGAGCTCAATTGGATTTTTACTGCTATAACAGATACAATTGCATGGAATGTTCTTCCTCATGgtatggcgtctgcgatgtatactttttggggatcaagaaaactagagaaaattattcaaattcaaaataaatgtcagcttattttgggtttatgatacaagtttcactgtgcag

Basic information

species Zea mays
transcript GRMZM2G048067_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048067_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 5'ss of exon 7
ATTCCTGGAAGGCAAAATGACCGTAAAACTCTTCTTGGGGAGCTCAATTGGATTTTTACTGCTATAACAGATACAATTGCATGGAATGTTCTTCCTCATGgtatggcgtctgcgatgtatactttttggggatcaagaaaactagagaaaattattcaaattcaaaataaatgtcagcttattttgggtttatgatacaagtttcactgtgcag
||||||||||||||||||||||| ||||||||||| |||||| | || |||||||| |||||||| ||||| || ||||||||||||||||||||||||||||  |           ||  | |||| |  |  |  ||  | || ||   | | |    |||  | | | | ||   ||| | ||   ||||||| ||| |||||||| ||||
ATTCCTGGAAGGCAAAATGACCGCAAAACTCTTCTAGGGGAGTTGAACTGGATTTTCACTGCTATCACAGACACTATTGCATGGAATGTTCTTCCTCATGgtactg----------atagtcgttttagttacaattaatgccagtga---tcaattgctttctcattcattttct-tttaatctg---ttatgattcaactttcactgcgcag

upper sequence: GRMZM2G048067_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 5'ss of exon 6
ATTCCTGGAAGGCAAAATGACCGTAAAACTCTTCTTGGGGAGCTCAATTGGATTTTTACTGCTATAACAGATACAATTGCATGGAATGTTCTTCCTCATGgtatggcgtctgcgatgtatactttttggggatcaagaaaactagagaaaattattcaaattcaaaataaatgtcagcttattttgggtttatgatacaagtttcactgtgcag
||||||||||||||||||||||| ||||||||||| |||||| | || |||||||| |||||||| ||||| || ||||||||||||||||||||||||||||  |           ||  | ||||    |  |  ||  | || ||   | | |    |||  | | | | ||   ||| | ||   ||||||| ||| |||||||  ||||
ATTCCTGGAAGGCAAAATGACCGCAAAACTCTTCTAGGGGAGTTGAACTGGATTTTCACTGCTATCACAGACACTATTGCATGGAATGTTCTTCCTCATGgtactg----------atagtcattttaatcacaattaatgccagtga---tcaattgctttctcattcattttct-tttaatctg---ttatgattcaactttcactacgcag

upper sequence: GRMZM2G048067_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA09G41510.1 (Glycine max), 5'ss of exon 7
ATTCCTGGAAGGCAAAATGACCGTAAAACTCTTCTTGGGGAGCTCAATTGGATTTTTACTGCTATAACAGATACAATTGCATGGAATGTTCTTCCTCATGgtatggcgtctgcgatgtata-ctttttggggatcaagaaaactagagaaaattattcaa--attcaaaataaatgtcagcttattttgggtttatgatacaagtt-tcactgtgcag------------
|| |||||  | | ||||||||| || || ||||| || ||  | |||||||| ||||| ||  |||| ||||| ||||| |||||||||||||||||||||| ||  ||  |  |    | | || ||  ||   |  ||| ||       || ||     ||    | | | |        ||||| ||| | | | |    |  | | | ||               
ATCCCTGGCCGTCCAAATGACCGAAAGACACTTCTGGGTGAATTGAATTGGATCTTTACAGCCGTAACTGATACGATTGCCTGGAATGTTCTTCCTCATGgta-ggtctcaaccctccccatccttctgccgacttactaaattaacatggtttttttttccatctccagtgatttagcatgcatttttggtatcttacattgatcattattttgttctgcactctgcag

upper sequence: GRMZM2G048067_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA18G44210.1 (Glycine max), 5'ss of exon 7
ATTCCTGGAAGGCAAAATGACCGTAAAACTCTTCTTGGGGAGCTCAATTGGATTTTTACTGCTATAACAGATACAATTGCATGGAATGTTCTTCCTCATGgtatggcgtctgcgatgtata-ctttttggggatcaagaaaactaga--gaaaattattcaa-----------attcaaaata-aatgtcagc-ttattttgggttta---tgatacaagtttcactgtgcag
|| |||||  | | ||||||||| || || ||||| || ||  | |||||||| ||||| ||  |||| ||||| ||||| |||||||||||||||||||||| ||  ||  |  |   || | || ||  ||      ||| ||    |  | || || |            |||||  ||  ||| |  |  || |||| |  |||   ||||     |||   | |||||
ATCCCTGGCCGTCCAAATGACCGAAAGACACTTCTGGGTGAATTGAATTGGATCTTTACAGCAGTAACTGATACGATTGCCTGGAATGTTCTTCCTCATGgta-ggtctcaactctccctatccttctgctgacttgctaaattaacatggtatttttttagcatctccagtgattcagcatgcaattttggtattttttttgtcttacattgatcattattttgttctgcag

upper sequence: GRMZM2G048067_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 7
ATTCCTGGAAGGCAAAATGACCGTAAAACTCTTCTTGGGGAGCTCAATTGGATTTTTACTGCTATAACAGATACAATTGCATGGAATGTTCTTCCTCATGgtatggcgtctgcgatgtatactttttggggatcaagaaaactagagaaaattattcaaattcaaaataaatgtcagcttattttgggtttatga-tacaagtttcactgtgcag
||||| ||  ||||||| || ||||| ||  |  | |||||| | || |||||||| || ||  | || ||||||||||| |||||||| |||||||||||||   | ||| | |     ||||| ||      ||   | | || | ||||  |     |||||  | | |      ||  | ||   | |||| |   ||||| ||  |||||
ATTCCAGGCCGGCAAAACGATCGTAAGACATTGTTAGGGGAGTTGAACTGGATTTTCACAGCAGTGACGGATACAATTGCTTGGAATGTGCTTCCTCATGgta---cttctccaa-----actttctgca---taatttatcaagggtaaatcttc----ttcaagttgacttct---tttctgtgtcctcatgaatgatagttttaccctgcag

upper sequence: GRMZM2G048067_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S199_73V6.1 (Physcomitrella patens), 5'ss of exon 7
ATTCCTGGAAGGCAAAATGACCGTAAAACTCTTCTTGGGGAGCTCAATTGGATTTTTACTGCTATAACAGATACAATTGCATGGAATGTTCTTCCTCATGgta---tggcgtctgcgatgtat--actttttggggatcaaga---aaactagagaaaattattcaaattcaaaat---aaatgtca---gcttattttgggtttatgatacaagtttcactgtgcag---------------------------
|| || ||  | ||||| || || || ||||   | |||||||| |||||||| || || |||||||||||||||||||| |||||||| || || |  |||    ||  || |   ||||    |  ||||  |  | || |   ||  |||||  |     | || || |||      ||  | |   | | ||||||| | |    |   | || |  | | |||                           
ATACCAGGTCGTCAAAACGATCGGAAGACTCCCTTGGGGGAGCTGAATTGGATATTCACAGCTATAACAGATACAATTGCGTGGAATGTGCTGCCGCGAGgtcagctgttgtttttcatgttcggatcttttttgtttgaaaatttaagttagaggtataacgtaaagttgaaagcttggaacataaaatggtcattttggatgtggtgtgataattacgatct-cagttagcatcttgcacttggacgacgcag

upper sequence: GRMZM2G048067_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S26_271V6.1 (Physcomitrella patens), 5'ss of exon 7
ATTCCTGGAAGGCAAAATGACCGTAAAACTCTTCTTGGGGAGCTCAATTGGATTTTTACTGCTATAACAGATACAATTGCATGGAATGTTCTTCCTCATGgtatggcgtctg---cgatgtat---actttttggggatcaagaaaactagagaaaattattca---aattcaaaataaatgtcagcttattttgggtttatgatacaagtttcac----tgtgcag--------------------------------------------------------------
|| || ||  | || |||||  | ||||||| | | |||||| | |||||||| |||||||||||||| ||||||||||||||||| || || || |  |||| |    |||   |    |||   | ||| |  |    |   |   |  |   | ||||| |   ||| ||  || ||        || ||||   ||  | |  ||  || ||    |||||||                                                              
ATACCCGGTCGTCAGAATGATAGGAAAACTCCTTTGGGGGAGTTGAATTGGATATTTACTGCTATAACTGATACAATTGCATGGAACGTGCTGCCGCGAGgtaagtaacctgaatctccttattcgattttattcgctgtatttattatttatttatttatttattgaatgcagcatcaacagttagataatttgacctttaggtgtaacattaaccaactgtgcagacttggctggtattcagtgtccgcgaactcgagcctttaacatctgaaacttatgaatgcag

upper sequence: GRMZM2G048067_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S124_156V6.1 (Physcomitrella patens), 5'ss of exon 7
ATTCCTGGAAGGCAAAATGACCGTAAAACTCTTCTTGGGGAGCTCAATTGGATTTTTACTGCTATAACAGATACAATTGCATGGAATGTTCTTCCTCATGgta------------tggcgtctg---cgatgtatactttttggggatc-------aagaaaactagagaaaattattcaaattcaaaataaatgtca-gcttattttgggtttatgatacaagtttcactgtgcag----------------------------
|| |||||  | |||||||| || || ||||   | ||||| || || ||||| ||||| ||||| |||||||||||||| ||||||||  | || |  |||             || ||| ||   | || | | |    ||    ||        | ||   ||   | | ||| |     | |     |   | | | | | | |  |  | |||||  |||       |                                
ATACCTGGGCGTCAAAATGATCGGAAGACTCCCTTGGGGGAACTGAACTGGATATTTACAGCTATCACAGATACAATTGCGTGGAATGTGTTGCCACGAGgtgagcagctactcttgacgtttgaacctattttttccccgtgatattctgtgagggataatgttatgaagacttagttgcgattacttggaccataaagttcactcttaggatgtgatatgagtaatgtaatcttaggtattctttggcaattcaatgacgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCCTGGAAGGCAAAATGACCGTAAAACTCTTCTTGGGGAGCTCAATTGGATTTTTACTGCTATAACAGATACAATTGCATGGAATGTTCTTCCTCATGgtatggcgtctgcgatgtatactttttggggatcaagaaaactagagaaaattattcaaattcaaaataaatgtcagcttattttgggtttatgatacaagtttcactgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA