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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctgtatcctttactgcatcttttcttttttctttctttatttctatgtcgttttaaagctaaaattagagagcttcatgcacttagacaagtcttgctgtgattttctatgtattccgcggataacttatcttgggtactgttttgtttttgcataatgttggcgatggggttacagATACATTCAAGGAAAATGAATGTGAATGCAGACGTCAATTTTGAAGAGCTTGCTCGGTCAACGGATGATTTCAATGGAGCTCAACTCAAAGCAGTGTGTG

Basic information

species Arabidopsis thaliana
transcript AT1G09100.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
gttctgtatcctttactgcatcttttcttttttctttctttatttctatgtcgttttaaagctaaaattagagagcttcatgcacttagacaagtcttgctgtgattttctatgtattccgcggataacttatcttgggtactgttttgtttttgcataatgttggcgatggggttacagATACATTCAAGGAAAATGAATGTGAATGCAGACGTCAATTTTGAAGAGCTTGCTCGGTCAACGGATGATTTCAATGGAGCTCAACTCAAAGCAGTGTGTG
                                                                      |   | |||  | || |    | ||||       |  |  | | |||||  |   |  ||| | |     ||   |     |||   |||| |  | | |     |  |||| || ||||| ||||||||||| ||  |||| || |||||||||||||| ||||| ||||| ||||| ||||||||||| ||||| ||||| || ||||
----------------------------------------------------------------------gtaggtttccagaacctgtg-atgtctaatc---agctaatgtttattcatccatttgcttttgtaatccacaagtcatgctttaactaatat--gtggttct-ctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 8
gttctgtatcctttactgcatcttttcttttttctttctttatttctatgtcgttttaaagctaaaattagagagcttcatgcacttagacaagtcttgctgtgattttctatgtattccgcggataacttatcttgggtactgttttgtttttgcataatgttggcgatggggttacagATACATTCAAGGAAAATGAATGTGAATGCAGACGTCAATTTTGAAGAGCTTGCTCGGTCAACGGATGATTTCAATGGAGCTCAACTCAAAGCAGTGTGTG
                                                                 ||| ||| ||      | | |    | || |   ||   ||   ||  |  ||  | || |  |  |      | |||     |||     |||| |  |      |   |  |||| || || |||||||||||||||||| |||| ||||| ||||||||| | || || ||||| |||||||||||||| ||||| || || || || || |
-----------------------------------------------------------------aataagaaag------ggatt----ctagcccccctccaatccccttcg-gttttgtggctcccaaact---agcactaaag-gttccaaaataacgccgatctatgttgtgtagATCCACTCGAGGAAAATGAATGTGAATCCAGATGTCAACTTTGAAGAGTTGGCGCGTTCAACCGATGATTTCAATGGCGCTCAGCTAAAGGCTGTTTGCG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 7
gttctgtatcctttactgcatcttttcttttttctttctttatttctatgtcgttttaaagctaaaattagagagcttcatgcacttagacaagtcttgctgtgattt-tctatgtattccgcggataacttatct-tgggtactgttttgtttttgcataatgttggcgatggggttacagATACATTCAAGGAAAATGAATGTGAATGCAGACGTCAATTTTGAAGAGCTTGCTCGGTCAACGGATGATTTCAATGGAGCTCAACTCAAAGCAGTGTGTG
                                                                      |   |  |||   |||||  |     ||||||   ||| ||  ||  || |     ||    || | |    |||    |||| |       | ||||   |     |  |||| |||||||||||||||||||| ||| | || ||||| ||||||||  | ||||| ||||| ||||| ||||| ||||| || || || ||||| ||||
----------------------------------------------------------------------gtcggtctcaacaacttatgctcaaattgctgaagtttgtcagtggctttcctcagtaggccatttatcacaactaacgtgttct------gtattggtcct----ctgtagATCCATTCAAGGAAAATGAATGTAAATCCTGATGTCAACTTTGAAGAATTGGCTCGCTCAACTGATGACTTCAACGGAGCACAGCTAAAGGCAGTTTGTG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 8
gttctgtatcctttactgcatcttttcttttttctttctttatttctatgtcgttttaaagctaaaattagagagcttcatgcacttagacaagtcttgctgtgattttctatgtattccgcggataacttatcttgggtactgttttgtttttgcataatgttggcgatggggttacagATACATTCAAGGAAAATGAATGTGAATGCAGACGTCAATTTTGAAGAGCTTGCTCGGTCAACGGATGATTTCAATGGAGCTCAACTCAAAGCAGTGTGTG
                                                                                                    | || | |  |     |||  | | | |||| | ||    || |     ||  ||  |  | |   |  ||   || ||||| ||||| ||||| ||||||||  |  |||| ||||| |||||||| ||||||||||| || ||||||||||||||||||||||| || || || ||||
---------------------------------------------------------------------------------------------------gtttggtgtctttaaacttcatctgctgacttgtttttcaaacagaacatttactgactgctctca-ctttgatatttcagATCCATTCGAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTTGCTCGGTCCACAGATGATTTCAATGGAGCTCAACTGAAGGCTGTTTGTG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 8
gttctgtatcctttactgcatcttttcttttttctttctttatttctatgtcgttttaaagctaaaattagagagcttcatgcacttagacaagtcttgctgtgattttctatgtattccgcggataacttatcttgggtactgttttgtttttgcataatgttggcgatggggttacagATACATTCAAGGAAAATGAATGTGAATGCAGACGTCAATTTTGAAGAGCTTGCTCGGTCAACGGATGATTTCAATGGAGCTCAACTCAAAGCAGTGTGTG
                                                                                                    |||  | ||| |    || | | | | ||  ||  |    |        |||    |  |   |  |  ||   ||  |||| ||||||||||| ||||||||  |  |||| ||||| |||||||| ||||| ||||| || |||||||||||||| || ||||| || || || ||||
-------------------------------------------------------------------------------------------------gtttgttgtcttccaaactttac-ctgctgacacattgttca-atcaaaacatttactgactaccctcactttgatattttagATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTTGCCCGGTCCACAGATGATTTCAATGGCGCACAACTGAAGGCTGTCTGTG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 8
gttctgtatcctttactgcatcttttcttttttctttctttatttctatgtcgttttaaagctaaaattagagagcttcatgcacttagacaa-gtcttgctgtgattttctatgtattccgcggataacttatcttgggtactgttttgtttttgcataatgttggcgatggggttacagATACATTCAAGGAAAATGAATGTGAATGCAGACGTCAATTTTGAAGAGCTTGCTCGGTCAACGGATGATTTCAATGGAGCTCAACTCAAAGCAGTGTGTG
                                                                               |||   | |   ||  | ||  | |   |   ||   |||     ||| |||  |    |      | |||  | |        ||  |  ||   ||  |||| || || || || |||| |||  || | || |||||||||||||| || ||||| || || |||||||||||||| || ||||| ||||| || ||||
-----------------------------------------------------------------------------gtatgtcttcaatgaatattttcttctagatcattacacatt-----gatcactctttgcagagctcttattgactct--------ttcacattgtatttgtagATCCACTCGAGAAAGATGACTGTTCATCCGGATGTCAATTTTGAAGAACTGGCTCGATCCACAGATGATTTCAATGGGGCACAACTGAAAGCTGTTTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacttatcttgggtactgttttgtttttgcataatgttggcgatggggttacagATACATTCAAGGAAAATGAATGTGAATGCAGACGTCAATTTTGAAGAGCTTGCTCGGTCAACGGATGATTTCAATGGAGCTCAACTCAAAGCAGTGTGTG
 ggataac  putative branch site (score: 3)
                   ttttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctgtatcctttactgcatcttttcttttttctttctttatttctatgtcgttttaaagctaaaattagagagcttcatgcacttagacaagtcttgctgtgattttctatgtattccgcggataacttatcttgggtactgttttgtttttgcataatgttggcgatggggttacagATACATTCAAGGAAAATGAATGTGAATGCAGACGTCAATTTTGAAGAGCTTGCTCGGTCAACGGATGATTTCAATGGAGCTCAACTCAAAGCAGTGTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA