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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttttcttatcggcaatgtcattacttctgatgttgacatttttctcattacttacatcactttgcaacagGCGTTGCTAGAAGCAATGGAACAACAATGTGTCTCTGTTGCAAAGGCTGGGCTTGTAGCTAGTCTATCAGCTCGAACTTCTGTTATAGCAGCAGCAAATC

Basic information

species Arabidopsis thaliana
transcript AT3G09660.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G09660.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g38850.1 (Oryza sativa), 3'ss of exon 9
------gttttttcttatcggcaatgtca----ttacttctgatgttgacatttttctcattac---ttacatcactttgca---acagGCGTTGCTAGAAGCAATGGAACAACAATGTGTCTCTGTTGCAAAGGCTGGGCTTGTAGCTAGTCTATCAGCTCGAACTTCTGTTATAGCAGCAGCAAATC
         || | | | |  || | | |    ||| ||   | |     |  |  | ||| |    |   || | ||||     | |||| || || ||||| ||||| || |||||||| ||||| ||||||||||| ||||| || ||| ||||||| || ||||||||  |||| || || ||||
gttttaaccttgtataagcttcactctgaaatgttaattagaaagccctaacctgccacatcatgtttctaatgaatttgagttcatagGCTTTACTGGAAGCCATGGAGCAGCAATGTGTATCTGTGGCAAAGGCTGGCCTTGTGGCAAGTTTATCAGCCCGTACTTCTGTGCTAGCGGCTGCTAATC

upper sequence: AT3G09660.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G163658_T01 (Zea mays), 3'ss of exon 8
------------------------------gttttttcttatcggcaatgtcatt-----acttctgatgttgacatttttctcattacttacatcactttgcaacagGCGTTGCTAGAAGCAATGGAACAACAATGTGTCTCTGTTGCAAAGGCTGGGCTTGTAGCTAGTCTATCAGCTCGAACTTCTGTTATAGCAGCAGCAAATC
                              | ||| || |   |       || |     | |||  |||   |  | ||| |  ||       |  ||      ||||| || || ||||| ||||| || |||||||| ||| ||||||||||||| |||||||| ||| | |||||||||||||| ||  | ||||| |||||||
gtattacaattatttttcaccttatatgaagctttctcatgaagttttcaccagtgaggaagttcccatgcctatctatttgtgtttctaattgtttctggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGTCTTGTAGCAAGTTTGTCAGCTCGAACTTCAGTGTTGGCAGCTGCAAATC

upper sequence: AT3G09660.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv08s0040g03290.t01 (Vitis vinifera), 3'ss of exon 9
----gttttttcttatcggcaatgt--catt--acttctgatgttgacatttttctcattacttacatc-actttgcaacagGCGTTGCTAGAAGCAATGGAACAACAATGTGTCTCTGTTGCAAAGGCTGGGCTTGTAGCTAGTCTATCAGCTCGAACTTCTGTTATAGCAGCAGCAAATC
    |   |  || |||    ||||  | ||  || ||| ||  | | |     | |||| || |  |  | ||| |  ||| |  | |||||||| ||||| ||||| ||||||||||||||||||||||| ||||| || ||| ||||||| |||||||||||  ||||||| |||||||
gtttggcctgactaatcattgatgtatcgtttgacctctaattgtca-agaccacacatttctaattttgagtttacctcagTCTCTTCTAGAAGCCATGGAGCAACAGTGTGTCTCTGTTGCAAAGGCTGGACTTGTGGCAAGTTTATCAGCACGAACTTCTGTCTTAGCAGCGGCAAATC

upper sequence: AT3G09660.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S16_310V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------gttttttcttatcggcaatgtcattacttctgatgttgacat-ttttctcattacttacatcactttgcaac---agGCGTTGCTAGAAGCAATGGAACAACAATGTGTCTCTGTTGCAAAGGCTGGGCTTGTAGCTAGTCTATCAGCTCGAACTTCTGTTATAGCAGCAGCAAATC
                       |||   | |  |  | | ||     |||   |    |  ||| || |||  |  | |||||       ||||   ||||  | || ||||| |||||||||||| |||| || |||||||||||||| ||||| || ||  |  |||| || || || ||  | || || |||||||
tattcagaagatatatgataattgttcgatttgtttagaactgggggaactgtgggaaatctcatgttctctgttctcatacatattgcaccaacttcagGCCCTACTTGAAGCTATGGAACAACAAAGTGTATCGGTTGCAAAGGCTGGACTTGTTGCCAGCTTGGCAGCACGTACATCAGTCCTTGCTGCTGCAAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcattacttctgatgttgacatttttctcattacttacatcactttgcaacagGCGTTGCTAGAAGCAATGGAACAACAATGTGTCTCTGTTGCAAAGGCTGGGCTTGTAGCTAGTCTATCAGCTCGAACTTCTGTTATAGCAGCAGCAAATC
                                 tacttac  putative branch site (score: 1)
                                         tcacttt  CT-rich tract
                    acattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttttcttatcggcaatgtcattacttctgatgttgacatttttctcattacttacatcactttgcaacagGCGTTGCTAGAAGCAATGGAACAACAATGTGTCTCTGTTGCAAAGGCTGGGCTTGTAGCTAGTCTATCAGCTCGAACTTCTGTTATAGCAGCAGCAAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC