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

gtaatcttgaaatggacgattttattcaaaatgtgtgatatgtctcctatggtgtgttgtgacgataaacctttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC

Basic information

species Arabidopsis thaliana
transcript AT3G08530.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 12
-----------------------gtaatcttgaaatggacgattttatt-caaaatgtgtgatatgtctcct---atggtgtgttg--tgacgataaacctttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC
                       ||    |  | ||   ||||||| || ||   |||    | || ||      || ||   ||   |||        || | || |  |||||||||| |||||||| ||||||||||||||||| || ||| |||| || || |||||||| || |||||||| ||||||||||| |||||||| || |
gtaaaatgggtgttaagttgtttgttgattgcacatat-cgattttgttacactgtgtcctgtttgactgtctggattgttcattaattgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 12
-----------------------gtaatcttgaaatggacgattttatt-caaaatgtgtgatatgtctcct---atggtgtgttg--tgacgataaacctttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC
                       ||    |  | ||   ||||||| || ||   |||    | || ||      || ||   ||   |||        || | || |  |||||||||| |||||||| ||||||||||||||||| || ||| |||| || || |||||||| || |||||||| ||||||||||| |||||||| || |
gtaaaatgggtcttaagttgtttgttgattgcacatat-cgattttgttacactgtgtcctgtttgactgtctggattgttcattaattgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
--------------------gtaatcttgaaatggacgattttattcaaaatgtgtg-atatgtctc--ctatggtgtgttgtgacgataaacctttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC
                     |  | ||||  |    |  |||  | ||| |   |  || |||||    ||| |    |  |  |    | |||||    |  |||||||||| |||||||| || ||||||||||||||||| ||  |||| || || |||||||| || |||||||| ||||| |||||||||||||||||||
gtaagatgggtcctatgctgtttttattgattttactgtattttgttaaattacatttatttgtcttggttatcgctaatcatttcttgtaccctttgatgtatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
---------gtaatcttgaaatggacgattttattcaaaatgtgtgatatgtctcctatggtgtgttg--tgac-gataaac-----ctttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC
         ||  |  |  |      ||| ||| |  |  |     || |   | |  |  ||| |||  ||   | |||       |  | |  |  |||||||||| |||||||| || |||||||||||||| || ||| |||| || || |||||||| || |||||||| ||||| |||||||||||||| | ||
tgtcataccgtgtttgttgatgcatggatcttactatactttgccaatttacattcacttatgtattggttgtttgctaagtgtgtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
gtaatcttgaaatggacgattttattcaaaatgtgtgatatgtctcctatggtgtgttgtgacgataaacctttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC-----------------
                       ||| | | |   | || | |     || || || |  |    |  || ||| |||   |||||||||| |||||||| || |||||||||||||| || ||| |||| || || |||||||| || || ||||| ||||| |||||||||||||| ||||                 
---------------------caatttacattcacttatgtattg---attgtttgctaagtgtgtgcacttttatgt---agactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 12
-----------------------------gtaatcttgaaatggacgatt--ttattcaaaatgtgtgatatgtc-tcctatggt-gtgttg--tgacgataaacctttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC
                              | | ||   | |  || | |  || || ||  ||  |  ||||   |  |||  | |||||   |     |||    |||  ||  ||||||||||||||||||| ||  | |||||||||||||||||  | || |||||||||||||| || |||||||| || ||||||||||||||||| || |
gttgggttgcatttataattttgcttttgtttacctaatagtatactactgcttgttgaatttgcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtagACTGTGGATAATGATCTTGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 12
-------------------------------------------------------------------gtaatcttgaaatggacgattttattcaaaatgtgtgatatgtctcctatggtgtg------ttgtgacgat-------aaacctttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC
                                                                    ||||  |  |    |   | | || |    |||   || ||  |  ||||   ||      |||||   ||       ||    |||  ||  |||||||||| |||||||| ||| | |||||||||||||||||  | || |||||||||||||| || |||||||| || ||||||||||||||||| || |
gttgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgcgtttgtttctttctaattgtttacctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtagACTGTGGACAATGATCTTGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 12
---------------------------------------------------------------------------------------gtaatcttgaaatggacgattttattcaaaatgtgtgatatgtc-tcctatggtgtgttg-tgacgataaacct-ttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC
                                                                                         ||| | |   |      | | ||  |   ||| |  | ||   |  | |  | | ||  |    | || | |  ||  ||  |||||||||| |||||||| ||| | |||||||| ||||||||  | || |||||||||||||| || || ||||| || || ||||||||||||||||| |
gttgggttgcattaaaattttgaaaaattcaatattattttgttatttataactttgcttgtactctatctttctaattgtctcccaaaaatataggggtactgattctcatctagcctgtttattgtgaaatgttgtattctattaatttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCATTTGCTGAGAGGAGGGAGTTTGACAAAATTC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 12
--------------------------------------------------------------------------gtaatcttgaaatggacgattttattcaaaatgtgtgatatgtctcctatggtgtgttgtgacgat------aaacct-ttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC
                                                                          ||   |   |||| |   | |  ||||  |   | | |  ||| |  | ||   ||||||    |       || | |  ||  ||  |||||||||| |||||||| ||| | |||||||| ||||||||  | || |||||||||||||| || || ||||| || || ||||||||||||||||| |
gttgggttgcattaaaatttgaaaaattcaatattattctgttatttataactttgtactctatctttctaattgtctgccaaaaatagggtactg-attctca---tctaacctgtttattgtgaaatgttgtattaacttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgtgtgatatgtctcctatggtgtgttgtgacgataaacctttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC
                                         cctttctgttcc  CT-rich tract
                                    ataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcttgaaatggacgattttattcaaaatgtgtgatatgtctcctatggtgtgttgtgacgataaacctttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG