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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactgaatactctatgaaaagttctaccgatttacacacgggatctttttttcaaacttgtgttcttcttaatactgcag

Basic information

species Arabidopsis thaliana
transcript AT4G24860.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactgaatactctatgaaaagttctaccgatttacacacgg---gatctttttttcaaacttg--tgttcttcttaatactg-cag
|||||||||||| ||||| || ||||||||||| || ||||| ||||  ||||| | ||| |||||||| ||||| |||||||||||||| ||||| ||||||       | || |      |   ||  ||  |  |||  |    || |  || |||||  |   || | || ||  ||||  |||
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggca-tccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcag

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GRMZM2G435582_T01 (Zea mays), 5'ss of exon 2
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactgaatactctatgaaaagttctaccgatttacacacgggatctttttttcaaacttgtgttcttcttaatactgcag
 ||||||||||| |||||||| || |||||||| |||||||| ||||  ||||| |  || || |||||||| || |||||||| ||||| ||||||||||||       ||   |||   |  |     |||| ||  || |  ||     |   |||  ||| | || ||||   | |||
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttcacctaatgggcaactgatgagattcac-tactgtctcaaggct---aaccagtggt-ttgttaacttt-cag

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GRMZM2G354532_T01 (Zea mays), 5'ss of exon 1
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactgaatactctatgaaaagttctaccgatttacacacgggatctttttttcaaacttgtgttcttcttaatactgcag
 ||||||||||| |||||||| || |||||||| |||||||| ||||  ||||| |  || || |||||||| || |||||||| ||||| ||||||||||||       ||   |||   |  |     |||| ||  || |  ||                                   
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttcacctaatgggcaactgatgagattcac-tactgtctcaag--------------------------------

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 7
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactgaatactctatgaaaagttctaccgatttacacacgggatctttttttcaaacttgtgttcttcttaatactgcag
 ||||||||||| |||||||| || |||||||| |||||||| ||||  ||||| |  || || |||||||| || |||||||| ||||| ||||| ||||||       ||   |||   |  |     |||| ||  || |  ||     |   |||  ||| | || ||||   | |||
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCGAAGgtattatttcacctaatgggcaactgatgagattcac-tactgtctcaaggct---aaccagtggt-ttgttaacttt-cag

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 13
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactgaatactctatgaaaagttctaccgatttacacacgggatctttttttcaaacttgtgttcttcttaatactgcag
 ||||||||||| ||||| || || |||||||| |||||||| ||||  ||||| | ||| || |||||||| || |||||||| ||||| || || ||||||       ||     |   |  |     |||| ||    |      |     | |||  ||| |    ||| |  | |||
CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttgacctagcgggcaactgatgagattcacttgtg----tctcaagcctaaccagtggttcgtttact--ttcag

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactgaatactctatgaaaagttctaccgatttacacacgggatctttttttcaaacttgtgttcttcttaatactgcag
||| || ||||| ||||||||||| |||||||| || || |||||||  || |||| ||| || ||||| ||||| || |||||||||||| | || ||||||  |    | |  |   ||   |||     ||  ||   | |    |   ||  | | | |      | || |  | |||
TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatcaattggac--aagcctctgttttttggcagttgagtatctgcattatagcatctaaataacctatt-ttccag

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GRMZM2G157621_T03 (Zea mays), 5'ss of exon 22
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactg---aatactctatgaa--aagttc--taccgatttacacacgggatctttttttcaaacttgtgttcttcttaatactgcag
||| || ||||| || || |||||||||||||| ||||| || ||||  || |||| ||| || || |||||||| ||||||||||||||  | || ||||||  ||   ||   | ||   |  |||||   | |||||||  |      ||   |||    |  ||     | | | | ||   |||
TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgtacttgtgcaacgttatactcatcaagtttgttcccgatttggagtacttattactttgctga--tttcaaccctgtaactataacag

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA04G37050.1 (Glycine max), 5'ss of exon 5
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgt--aactgaatactctatgaaaagttctaccgatttac-acacgggatctttttttcaaacttgtgttcttct----taatactgcag
||| || |||||||| || ||||| ||||||||||| ||||| || |  ||||||| ||| || ||||||||||| || |||||||| ||||||||||||||  || |   | | ||  |   | ||  |    | | | |   |  |  | ||  |   |  ||||||||| |    |  | || |||
TGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTTCCATGTCAAGTATCACATCTAAGgttaaatttgcttcactgggtttattttaatgtctctgctatcagttagttgttcattttatctgtgttcttttcccattttgcttcag

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA17G13850.1 (Glycine max), 5'ss of exon 20
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactgaatactctatgaaaagttctaccgatttacacacgg--gatctttttttca---aacttgtgttctt----cttaatactgcag
||| || ||||||||||| || || ||||||||||| ||| | || |  ||||||| ||| |||||||||||||| || |||||||| |||||||||||||| |       |||| |  ||   | ||  |||||   |        | |  | | ||   ||||  | |||||    |||  | || |||
TGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTTCTATGTCAAGTATCACATCTAAGgttaaatttgtctctctctaagtgtatattgatttcacctttattagtttgctgtgcatacaactcattttcttgcctctttttgcttcag

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA06G17940.1 (Glycine max), 5'ss of exon 22
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactgaatactctatgaaaa--gttctaccgatt----tacacacgggatctttttttcaaacttgtgttcttcttaat--actgcag
||| || |||||||| || ||||| ||||||||||| ||||| || |  ||||||| ||| || ||||||||||| || |||||||| |||||||||||||| |    || ||  |         || ||  |  |    ||       | | ||  ||| ||     |  | |||  | |   || |||
TGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTTCCATGTCAAGTATCACATCTAAGgttag-atatgcttcactgggtttattttaatgtctctgttatcagttagttgttcattttaactgcattcttttcccattttgcttcag

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA05G03270.1 (Glycine max), 5'ss of exon 18
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactgaatactctatgaaaagttctaccgattt-acacacgggatcttttttt-----caaacttgtgttctt----cttaatactgcag
||| || ||||||||||| || || ||||| ||||| ||| | || |  ||||||| ||| |||||||||||||| || |||||||| || || |||||||| |       | || |  ||   | ||  ||| | ||       |  ||  | |       ||||  |||||||    ||   | || |||
TGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttgtccctctccaagtgtatattgatctcacctttattagtttgctgtgcatatcaactcatgttcttgcccctctttgcttcag

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaac---tgaatactctatgaaaagttctacc----gatttacacacgggatc--------tttttttcaaacttgtgttctt---cttaatactgcag
||| || |||||||| || ||||| |||||||| || || || || |  ||||||| ||| ||||||||||| || |||||||||||||||||||||||||| |    |||  | |   |      ||||| |    ||| |  | |  || |         ||||||||  |  ||  ||||     ||  |  |||||
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactgaatactctatgaaaagttctaccgatttacacacgggatctttttttcaaacttgtgttcttcttaatactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT