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'   		29  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtagtttctttagacttttgttaaatatggtaggattttcatgaaagaattatatatgcgatcccttttgtagGTGAATCCTGGGAATGCTCCCTTAGTTGTGGGGCAGTTGCTTGATGACGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTTTCTGTTCGTTCATTAC

Basic information

species Arabidopsis thaliana
transcript AT3G11130.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 21
gtatgtagtttctttagacttttgtta--aatatggtaggattttcatgaaagaattatatatgcgatccctt---------ttgtagGTGAATCCTGGGAATGCTCCCTTAGTTGTGGGGCAGTTGCTTGATGACGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTTTCTGTTCGTTCATTAC
||||| |  |  |  |      |||||      |   |  ||| |||||    |  ||| ||   | |   ||         ||||||||||| ||||| |||||||| |||||||| || ||| | |||||||| || |||||||||||||| || || ||  | ||||| ||||| |||||  | |
gtatgcaactcttccaattcagtgttattggagtatcatcattctcatgtgctatgtatttaaatgcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
gtatgtagtttctttagacttttgtta--aatatggtaggattttcatgaaagaattatata------tgcgatccctt---ttgtagGTGAATCCTGGGAATGCTCCCTTAGTTGTGGGGCAGTTGCTTGATGACGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTTTCTGTTCGTTCATTAC
||||| |  |  |  |      |||||      |   |  ||| |||||    |  ||| ||      |    ||| ||   ||||||||||| ||||| |||||||| |||||||| || ||| | |||||||| || |||||||||||||| || || ||  | ||||| ||||| |||||  | |
gtatgcaactcttccaattcagtgttattggagtatcatcattctcatgtgctatgtatttaaattcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 1
-----------------gtatgtagtttctttagactt-----ttgttaaatatggtaggattttcatga-aagaattatatatgcgatcccttttgtagGTGAATCCTGGGAATGCTCCCTTAGTTGTGGGGCAGTTGCTTGATGACGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTTTCTGTTCGTTCATTAC
                 || | | |  ||| |  | |      | |||    ||  |||| |    |||| ||   |||  | |    ||   |||  |||||||||| ||||||||||| || || |||||||| || |||||||| |||||||||||||||||||| || ||  | || || |||||||||||  | |
gttcagaaggtagttgtgtgtttcgactctgttaattcgtgcgtcgttcctcataataggttgagtatgagaatggttaattcttttttcttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTGAAGATTTTATCAAGGGTTTGATCCTCTCTGTTCGTTCTCTCC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 7
--------gtatgtagtttctttagactt-----ttgttaaatatggtaggattttcatga-aagaattatatatgcgatcccttttgtagGTGAATCCTGGGAATGCTCCCTTAGTTGTGGGGCAGTTGCTTGATGACGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTTTCTGTTCGTTCATTAC
        || | | |  ||| |  | |        |||    ||  |||| |    |||| ||  ||||  | |     |   |||  |||||||||| ||||||||||| || || |||||||| || |||||||| ||||||||| |||||||||| || ||  | || || | |||||||||  | |
gtagttgtgtgtttcgactctgttaattcgtgcgccgttcctaataataggttgaatatgagaacgattaattctttttccttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTAAAGATTTTATCAAGGGTTTGATCCTATTTGTTCGTTCTCTCC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 19
gtatgtagtttctttagacttttgttaaatatggtaggatt-ttcatg---------aaagaattatatatgcgatcccttttgt---------agGTGAATCCTGGGAATGCTCCCTTAGTTGTGGGGCAGTTGCTTGATGACGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTTTCTGTTCGTTCATTAC
|||||||  | ||| |      |||||  |  ||    ||| |||||          ||  | || | |    | | ||||||||         |||| |||||||| ||||||||||| || || |||||  | || ||||| |||||||| |||||||| || || ||  | ||||| |||||||||||  | |
gtatgtacatccttgaagtcactgttattttgggcgtcattcttcatctggtatttcaagcatttgtttgattgtttccttttgtcttgtatgtagGTCAATCCTGGTAATGCTCCCTTGGTAGTTGGGCAACTTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 21
gtatg-tagtttctttagacttttgttaaatatggtagg---attttcatgaaagaattatatatgcgatcccttttgta--gGTGAATCCTGGGAATGCTCCCTTAGTTGTGGGGCAGTTGCTTGATGACGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTTTCTGTTCGTTCATTAC
||||  ||||  | ||     | |  | | |    |       |||||       |  || |  | ||  || || | ||  |||||| || |||||||| || |||||||| |||||| |||| ||||| |||||| | ||||||||||| |||||| | || |||||||||||||||||||
gtataatagtagccttgcttatctcatgagtgctatctactctttttctctgcctatgtaaaacttcgtgcctttctatacagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAATGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTAC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 21
gtat----gtagtttctttagacttttgttaaatatggtaggattttcatgaaagaattata--tatgcgatcccttttgtagGTGAATCCTGGGAATGCTCCCTTAGTTGTGGGGCAGTTGCTTGATGACGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTTTCTGTTCGTTCATTAC
||||    |||| ||   |   ||  || |   |||       |||||       |  || |  | || |      | |  ||||||| || |||||||| || |||||||| |||||| |||| ||||| || ||| | ||||||||||| |||||| | || |||||||||||||||||||
gtataatagtagctttgcttatctcatgattgctatctactctttttctctgcctatctaaaactttgtgcctttctatacagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAGTGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTAC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 20
-------------------gtatgtagtttctttagacttttgttaaatatggtaggattttcatgaaagaattata-tatgcgatcccttttgtagGTGAATCCTGGGAATGCTCCCTTAGTTGTGGGGCAGTTGCTTGATGACGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTTTCTGTTCGTTCATTAC
                     |||  ||    ||     ||    |||||   |    |||   ||    | | |||  ||     |   ||| |||||||| || ||||||||||| ||||| || |||||| |  | ||||| |||||||| ||||||||||| |||||| | ||||| ||||||||||| ||||
gtattatagtttgcattaataatgctgtaatcttgcttattacacaaatactatctactttctctgccccactcataacattgtgccttctttatagGTGAACCCAGGGAATGCTCCTTTAGTCGTTGGGCAGCTTTTAGATGATGAATGCCCAGAAGATTTTATCAAAGGCTTGATTCTCTCTGTTCGTTCCTTAC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 20
--------------------------gtatgtagtttctttagacttttgttaaatatggtaggattttcatgaaagaattata--tatgcgatcccttttgtagGTGAATCCTGGGAATGCTCCCTTAGTTGTGGGGCAGTTGCTTGATGACGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTTTCTGTTCGTTCATTAC
                          |||       | |||| |    |  ||  ||   |    |||   ||    | | |||  | || |     |||| |||||||| || ||||||||||| ||||| || |||||| |  | ||||| ||||| || ||||||||||| |||||| | ||||| ||||||||||| ||||
gtattatagtttgcattaataatgctgtaaccttgctttttacatgaatactatctagtatctactttctctgccccactcataactttgtgccttgttttatagGTGAACCCAGGGAATGCTCCTTTAGTCGTTGGGCAGCTTTTAGATGATGAATGTCCAGAAGATTTTATCAAAGGCTTGATTCTCTCTGTTCGTTCCTTAC

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 21
--------------------------------------------------------gtatgtagtttctttag-acttttgttaaatatggtagg-attttcatgaaagaatta--tatatgcgatcccttttgtagGTGAATCCTGGGAATGCTCCCTTAGTTGTGGGGCAGTTGCTTGATGACGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTTTCTGTTCGTTCATTAC
                                                           ||| | | ||| |   |  |  |||| | | ||    | ||   |||   |||||  |   |  | | |  ||  |||||||| ||| | ||||| || ||||||||||||||| |||| ||||| ||||| || |||||||| || ||||| || ||||||||||| || ||  | |
gtgtgagttccttctagaattctagaattttggatcccctttgggtcatgatgaactcctgtggatgcttcaatgccctaattaattttagtcttcaattatttgattaaattaattgcttttgcttctcttgatagGTGAACCCTAGTAATGCACCTTTAGTTGTGGGGCAGCTGCTAGATGATGAATGTCCAGAAGATTTCATTAAAGGTCTAATTCTTTCTGTCCGGTCGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaaatatggtaggattttcatgaaagaattatatatgcgatcccttttgtagGTGAATCCTGGGAATGCTCCCTTAGTTGTGGGGCAGTTGCTTGATGACGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTTTCTGTTCGTTCATTAC
                                           tcccttttgt  CT-rich tract
                attttcatgaaagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtagtttctttagacttttgttaaatatggtaggattttcatgaaagaattatatatgcgatcccttttgtagGTGAATCCTGGGAATGCTCCCTTAGTTGTGGGGCAGTTGCTTGATGACGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTTTCTGTTCGTTCATTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA