Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttggtattgagaaaatcgtatataatactcttcttgaagtaacaatcattggtaatttttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG

Basic information

species Arabidopsis thaliana
transcript AT5G55160.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G55160.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G082390_T02 (Zea mays), 3'ss of exon 1
---------------------------gtttttggtattgagaaaatcgtatataatactcttcttgaag--taacaatcattggtaatttttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG
                             ||||| ||| |  ||  ||   | | ||      |||||    |  | ||| ||  ||||  |  |||| |||||||| ||||| || |||||| | || |||||   ||| ||||| || || |||||||| ||||| |||||||| |||||||||||  | ||  | ||||
ttacatgtcatattgaaaaggttacacacttttgatatcgc-aatctcaagtgttatctgtcacttgactcttttccatcttta-taataataattgtatagGATGGCAATGAGGTGTTCTTTCGCATAAAGAGGTCCACCCAGCTGAAGAAGCTGATGAACGCTTATTGTGACCGCCAGTCTGTGGACATGAATGCCATTG

upper sequence: AT5G55160.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G46500.2 (Glycine max), 3'ss of exon 1
---------------------gtttttggtattgagaa--aatcgtatataatactcttcttgaag---taacaatcattggtaattt-ttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG
                      | | |   | |   ||   ||  |||     | | |  ||  |    |  ||    || ||  ||   | ||||||||||||||||||| || ||||||||||| || ||||||||||||||||| ||||| |||||||| |||||||| ||||| ||||| ||||| ||||||||||
tactatctttaacccaactgattatctcacaatataaatttattttatgggggaatttctttacaaatttttcatctttttgtggttgacttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTTATGAATGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG

upper sequence: AT5G55160.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G35450.1 (Glycine max), 3'ss of exon 1
------------------------gtttttggtattgagaaaatcgtatataatactcttcttgaagta--acaatcattggtaattt-ttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG
                          |     |||  |   | |  |       | |  | |  || |    ||    || ||  ||   | || |||||||||| ||||| || ||||||||||| || ||||||||||||||||| ||||||||||| || |||||||| ||||| ||||| ||||| ||||||||||
actatcttaacccaactgactttatctcacaatataaatttattttttgggggaatttctttacaaattttccatctttttgtggttgacttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG

upper sequence: AT5G55160.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0186g00020.t01 (Vitis vinifera), 3'ss of exon 1
------------------gtttttggtattgagaaaatcgtatataatactcttcttgaagtaacaatcattggtaatttttc---------ttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG
                  |||||   |         | | |    | | | |  |   |      |||  |||  || ||||          |||  ||||||||||| || || |||||||||||||| |||||||| ||| |    || || |||  |||||| ||||| || ||||| ||||| || ||||| ||||
atggatgactctcctcctgttttcttttcaactcctagcattcccattcccccaccccacaagtgaatttttgtaaaatttttattttgtggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTATTGTGATCGACAGTCAGTGGAGTTAAACTCCATTG

upper sequence: AT5G55160.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0059g01310.t01 (Vitis vinifera), 3'ss of exon 1
---------------gtttttggtattgagaaaatc---gtatataatactct-----tcttgaa----gtaacaatcattggtaatttttcttgt-gtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG
               |  ||||| | | | || |||   || |  | |   ||     || || |     | || |  ||  ||  | ||| || | | ||||||| |||||||| ||||| |||||||| |||||||| ||||| || || || ||||||||||| |||||||| || ||||| ||  ||||||| ||||
gggagcaagttctaagaatttgg-actaaaaatatctctgtttgcagtttgctaggtttcctggacaagatgacgaggatgtgttgtgttttttattgcagGATGGGAATGAAGTTTTCTTCAGGATCAAAAGAAGCACACAGCTGAAGAAGCTCATGAATGCTTATTGTGACCGACAATCTGTAGACCTCAACTCGATTG

upper sequence: AT5G55160.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0186g00080.t01 (Vitis vinifera), 3'ss of exon 1
------------------------gtttttggtattgagaaaatcgtatataatactcttct--tgaagtaacaatcattggtaatttttc-ttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG
                         ||||     |  |  |   |     |  ||| |  |   |||| |       | || |  ||| |  |||||||||||||||| || || |||||||||||||| |||||||| ||| |    || || |||  |||||||||||| |||||||| ||||| || ||||| ||||
tatggatagttctgctcttgttttcttttcaacttccaccattcccatccttgtaccccacaagtgaatttttttaaaatgttcttttctggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTACTGTGATCGTCAGTCAGTGGAGTTAAACTCCATTG

upper sequence: AT5G55160.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S61_57V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------gtttttggtattgagaaaatcgtata-taatactcttcttgaagtaacaatcattggtaatttttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG
                                ||   || |  |  | ||     | | |||||   |   |||  | || |        |||   | || ||||||||||    || || |||||||||||||| || |   |     |    || |||||||| |||||||||||||| ||||||||||||     ||| ||||
gttggcacgctttttcaagggataaaactaaggtgcctgttggtatgcaatatacagaataatatgttctgtgagctgacga------aaaatcagtgttttgtagGATGGAGGGGAGGTGTTCTTTAGGATCAAAAGCACTGCCACTTTGCGCAAGCTGATGAACGCTTACTGTGACCGCCAGTCTGTGGATCCTTCCTCTATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgtatataatactcttcttgaagtaacaatcattggtaatttttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG
                      aagtaac  putative branch site (score: 2)
                                         tttttcttgt  putative PPT
                                      taatttttctt  TA-rich tract