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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtgcatatatgttggttactctgatttggaagttgttatgaactggattctaatgatggttgctaacatcgtaatactagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAA

Basic information

species Arabidopsis thaliana
transcript AT1G52360.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 15
----gtattgtgca-tatatgttggttactctgatttggaagt-tgttatgaactggattctaatgatggttgctaacat----cgtaatac-----tagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAA
     |||||||   |  |||   |    | |  ||||  | | | || |  | || | | |  ||     | | ||  |    |||  |||      |||| ||||| |||||||| ||||| ||||| ||||| |||||||||||||| || | |||||| || ||||   |  | ||||| ||||||||
gtatatattgtgtgctccatgcaagaatttttattttgttaatgtattttctattgtagtattttgtgcactacaaatttatcccgttgtacatttacagGTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAA

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
-------------------gtattgtgcatatatgttggttactctgatttggaagtt---gttatgaactggattctaatgatggttgctaacatcgtaatactagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAA
                     |   | | | | | |   || ||||   | || | ||   || ||||  |  |||      || |||   | | |  || |   |||| || ||||||||||||||||| ||||| ||||| |||||||||||| |||| |  |||||||| ||||   |  | ||||| || || ||
gtaaatatagtctgctcgaaaacatttcttctgtttaaatt-ctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G095348_T03 (Zea mays), 3'ss of exon 15
-----------------------------gtattgtgcatatatgttggttactctgatttggaagttgttatgaactggattctaatgatggttgctaacatcgtaatactagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAA
                              | || ||  ||  |  |   ||     | || |     || | ||  |  ||| |    |  |||   | | | ||| |   |||| || ||||||||||||||||| ||||| |||||  | |||||||||||||| |  |||||||| ||||   |  | ||||| || || ||
gtaaaaatagtctactccttgaaaacgttttcttctgtttaagttctctatatggccactttgtga--gtcacgacttcaattgtttacacagttataagctttgtacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACCTATTGGGATATCTTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTTAA

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 15
--------------gtattgtgcatatatgttggttactctgatttggaagttgttatgaactggattctaatgat-------------ggttgctaac-atcgtaatactagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAA
                 || |  || | |  |    |    || |||    || || | || || | |   | |||             | |   |||  ||  | |   |||||||| || |||| ||||||||||||||| ||||| |||||||||||||||||||  |||||||| ||||  ||| | |||||||| || ||
gtattaactcttttcccttctagatttctagtttaaaaaaagaattgtgcattctttttaattgaactacgaggatcatgagacatcttgatacataatgattatgaatttagGTAACTACGATGTTTCATTTGGACCGCCCTATGTACTTGTTGGGATATCTTGCAAACCAAAGTCGTGTTTATTTGATTGACAAAGAGTTTAA

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA13G43680.1 (Glycine max), 3'ss of exon 15
---------------------------gtattgtgcatatatgttggttactctgatttgg--aagttgttatgaac-tggattctaatgatggttgctaacatcgtaatactagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAA
                            || | |  | |    |||   | |||  |||     |  |   | || | ||     |  |||||  |  | |  |  | |   |||||||| || |||| ||||||||||||||| ||||| |||||||||||||||||||  |||||||| ||||  ||| | |||||||| || ||
gtattaactcttttcccttctagatttctagtttaaaaaagaattgtgcattcttttttaattgaactacaaggatcatgagacatcttgatgcataatga--ttatgaatttagGTAACTACGATGTTTCATTTGGACCGCCCCATGTACTTGTTGGGATATCTTGCAAACCAAAGTCGTGTTTATTTGATTGACAAAGAGTTTAA

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------gtattgtgcatatatgttggttactctgatttggaagttgttat-gaact----ggattcta--atgatggttgcta----acatcgtaatactagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAA
                                                                  ||  |   | | | ||  | | | |  | |     |  |||| |||||    ||||  ||  ||    |||| |     ||||  |     ||||| || ||||||| |||||||||||| || ||||| ||||||||||||||||| || ||||||  ||| |  ||| ||||||||||||||||
gtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgttgcattacattatggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAA

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 15
----------------------------------------------------------------gtattgtgcatatatgttggttactctgatttggaagttgttat-gaact----ggattctaa------tgatggttgctaacatcgtaatactagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAA
                                                                  ||  |   | | ||||| | | | |  | |     |  |||| |||||    ||||  ||       || || |   | ||||  | |   ||||| || ||||||| |||||||||||| || ||||| ||||||||||||||||| || ||||||  ||| |  ||| | ||||||||||||||
gtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAA

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 15
-------gtattgtgcatatatgtt----ggttactctgatttg-gaagttgttatgaact----ggattctaatga---tggttgctaac--atcgta-atactagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAA
       ||||||| ||    |||        || |   || || | || || |||  | |    |||||     ||   |  ||| |||   | | ||  | | ||||||||||||||| |||||||||||| || |||||||||||||||||||| || | |||||| ||||| |   |  |||||||||| |||||
gtattgtgtattgtccacccttgtcttgaaagtatttccatatgtgcagatgatatccatttcatggatttcttggagcttttttgttaaataaccatatgttccagGTAACCACAATGTTTCATTTGGACCGGCCTATGTATTTGTTGGGATATCTAGCTAATCAAAGCCGGGTGTATCTCATAGACAAAGAGTTCAA

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 15
--------gtattgtgcatatatgttggttactctgatttggaagttgttatgaactggattctaatgatggttgctaacatcgtaatactagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAA
        |  |||     |  |  |  ||      || ||    |  || | |  || | ||  || |   ||| |||  |  | ||   |||||||||| |||| ||| |||||||| || ||||||||||| ||||||||||| ||||||||||| ||||   |  |||||||||| || ||
gtataagagagttgattccaggttgtatttctatatatatgatcttcattctaaggtgcagtcatataa--attgttaatgtgatgatttcagGTAACCACCATGTTTCACTTGGACCGGCCTATGTATTTGTTAGGATATCTTGCCAGTCAAAGTCGCGTTTATCTTATAGACAAAGAGTTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaagttgttatgaactggattctaatgatggttgctaacatcgtaatactagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAA
                                   tgctaac  putative branch site (score: 1)
                     attctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtgcatatatgttggttactctgatttggaagttgttatgaactggattctaatgatggttgctaacatcgtaatactagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA