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

gtaagtttattatctcagatatgttctcagtagatatcattcaagtcgttcatgaaatactgacaacagaatctatgtagCTTCTCGTTTATTTCAGGCGTTTCTGGAACCAGTCTTTTCAATTCAGTTAGCCTGATGGCTTATAACGTTTTCTACACCAGTGTTCCTGTTCTTGTTAGT

Basic information

species Arabidopsis thaliana
transcript AT5G44240.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 21
---------------------------------------------------gtaagtttattatctcagatatgttctcagtagatatcattcaagtcgttcatgaaatactgacaacag--aatctatgtagCTTCTCGTTTATTTCAGGCGTTTCTGGAACCAGTCTTTTCAATTCAGTTAGCCTGATGGCTTATAACGTTTTCTACACCAGTGTTCCTGTTCTTGTTAGT
                                                    ||   || | |   ||  |||  | | |    ||       |  |  |||    |  | ||    ||    ||  ||| || || || ||| |||| ||  || ||||||| ||||| ||||| || |||||  |||||||||||||||| |||||||| ||  ||||||||||   || |
gtaagtcaaacttagtctggcatctttttgcttatttgagttcttaatgcaatagtattctcagtccatttat-ctgtaaaagaatgctggatatatgcttctcttatcaatgttctcattttatgcatgcagTTTTTCTTTTCTTTCTGGTATTGCTGGAACAAGTCTATTCAACTCGGTTAGTTTGATGGCTTATAACGTCTTCTACACAAGCATTCCTGTTCTAACTACT

upper sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G479163_T01 (Zea mays), 3'ss of exon 3
-------gtaagt--ttattatctcagatatgttctcagtagatatcattcaagtcg--ttcatgaaatactgacaacagaatctatgtagCTTCTCGTTTATTTCAGGCGTTTCTGGAACCAGTCTTTTCAATTCAGTTAGCCTGATGGCTTATAACGTTTTCTACACCAGTGTTCCTGTTCTTGTTAGT
        |||    |   ||  |    |||| |    | |  |||  |    |     ||  |  | | || | |      |  ||| || || || ||| |||||||| || ||||||| ||  | ||||| ||||||||  ||||||||||||| ||||||||||| ||  |||||||| |   || |
gtaagccataaaccgtccgtacttgtattatggtagttggacgtatagtgtgtgctagttttcttgattgctcatattctg-tgcatgcagTTTTTCTTTTCTTTCAGGCATTGCTGGAACAAGCTTATTCAACTCAGTTAGTTTGATGGCTTATAATGTTTTCTACACAAGCATTCCTGTTTTAACTACT

upper sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G037335_T01 (Zea mays), 3'ss of exon 7
--------------------------------gtaagtttattatctcaga--tatgtt-ctcagtagat-atcattcaagtcgttcatg-aaatactgacaacagaatctatgtagCTTCTCGTTTATTTCAGGCGTTTCTGGAACCAGTCTTTTCAATTCAGTTAGCCTGATGGCTTATAACGTTTTCTACACCAGTGTTCCTGTTCTTGTTAGT
                                 |   ||| | ||  ||    |||| | ||  | |  |   |||     | ||   || || | || ||   ||   |  | ||| ||  | ||| | || ||  | ||||| || ||  | ||||| ||| ||||| |||||||||||||||||||||| || ||| | || ||  |   ||  
gtgagttttccttgtaatgcttatgccattggctgcatttttcattacaagcttatgctactttgcactttggcatgggttttgtgggtgcaactgctcacttgagtccccttttagGTTTGCCTTTTTGTCGGGGCTATCTGGGACTAGCTTATTCAACTCAATTAGCTTGATGGCTTATAACGTTTTCTATACAAGTTTACCCGTCATGACTATA

upper sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 21
-------------gtaagt-ttattatctcagatatgttctcagt----------agatatcattcaagtcgttcatgaaatactgacaacagaatctatgtagCTTCTCGTTTATTTCAGGCGTTTCTGGAACCAGTCTTTTCAATTCAGTTAGCCTGATGGCTTATAACGTTTTCTACACCAGTGTTCCTGTTCTTGTTAGT
              | | | || | ||   ||||  |    || |          |||| |  |  || |  ||||  |  ||||||  |  | || |    || || || ||||||||||| || |||||||| || || |||||||| |||||| ||||||||||||| |||||||| || |||||||||||||| ||||||
attgttaatgattatgaatgttctaatgctagatgggcatccaatttctttatatagatctattctaaatttttca--aggtactgatgattgcattttc--agTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTTAGT

upper sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA13G37090.1 (Glycine max), 3'ss of exon 21
------------gtaagt-ttattatctcagatatg---------ttctcagtagatatc-attcaagtcgttcatgaaatactgacaacagaatctatgtagCTTCTCGTTTATTTCAGGCGTTTCTGGAACCAGTCTTTTCAATTCAGTTAGCCTGATGGCTTATAACGTTTTCTACACCAGTGTTCCTGTTCTTGTTAGT
             | | | || | ||   ||||| |         ||||   || | ||| |||| |    ||  | |  ||||||     |   || |  || || || ||||||||||| || |||||||| || || |||||||| |||||| ||||||||||||| |||||||| || |||||||||||||| || |||
ttgttactgattatgaatgttctaatgctagataggcattccaatttctttatatagatctattctaaaaattt-taaggtactgatggttg--ccttttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcagtagatatcattcaagtcgttcatgaaatactgacaacagaatctatgtagCTTCTCGTTTATTTCAGGCGTTTCTGGAACCAGTCTTTTCAATTCAGTTAGCCTGATGGCTTATAACGTTTTCTACACCAGTGTTCCTGTTCTTGTTAGT
                                tactgac  putative branch site (score: 1)
        atatcatt  TA-rich tract