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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattagcatgcatgcaagttgatcgaagaatcaaaaaaatcaaagttaggtttgcgattgaattgagcatccaacatgtacaaatattgcagAGAAGTGCAAGATTGGCATGGAAGAACAGAATGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCGACGGGCACCCGCACCAACCGGGCCACGGG

Basic information

species Oryza sativa
transcript LOC_Os02g42970.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g42970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G354151_T01 (Zea mays), 3'ss of exon 3
gtaattagcatgcatgcaagttgatcgaagaatcaaaaaaatcaaagttaggtttgcgattgaattga-gcatccaacatgtacaaatattgcagAGAAGTGCAAGATTGGCATGGAAGAACAGAATGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCGACGGGCACCCGCACCAACCGGGCCACGGG
     ||  | | |    | ||     |  | |  | | |  || |  |||   |||   | ||| ||  ||| ||   || |       |||||||||||||||||| || | ||| || ||||| || |||||||||||||||||||| ||||| ||||||||||||||||||||||| |||||||| ||   
----gtaagaagtacattaattctgaaacaagtatatatatacatacatag--ctgctgctaaatagacacatgcattttggaatgggcatgcagAGAAGTGCAAGATCGGGACGGAGGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGCACCCGCACAAACCGGGCGACCAC

upper sequence: LOC_Os02g42970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G315140_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------gtaattagcatgca--tgcaagttgatcgaagaatcaaaaaaatcaaa-gttaggtttgcgat--tgaattgagcatccaacatgtacaaatattg--cagAGAAGTGCAAGATTGGCATGGAAGAACAGAATGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCGACGGGCACCCGCACCAACCGGGCCACGGG
                                             ||   ||| |  ||  | || |   ||  |    |      ||| |||  ||||  |  | ||  | ||||| |||||  ||||| |     | ||  ||||||||||||||||||| ||||| || ||||| || |||||||||||||||||||| ||||| ||||||||||||||||| |||||||||||||| ||   
gcaagaaataaatacattccgaaagcaagtagttgatgcaatggagttggtagtagacaattacatgcatatatacacgtgctgctaattaaatattagactcacaatgatcaattg-gcatcacacatgcatttggaatgggcagAGAAGTGCAAGATTGGGATGGAGGAGCAGAACGATTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGCACTCGCACCAACCGGGCGACCAC

upper sequence: LOC_Os02g42970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------------------------gtaattagcatgcatgcaagttga--tcgaagaatcaaa--aaaatcaaagtt-aggtttgcgattgaattgagcatccaacatgtacaaatattgcagAGAAGTGCAAGATTGG--------CATGGAAGAA-CAGAATGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCGACGGGCACCCGCACCAACCGGGCCACGGG
                                                                                        || | ||  || |  || | ||   ||||    |   |    ||| | | |  | ||   | |   |   |  ||   |||    |         ||||   ||||| ||||||        ||    |||| || || ||||||||||||||||||||||||||||||||||||||  ||||||  ||  | |||||         
gtaagaatcgatcagaatcctcggtgtactatgtatgacaccagactagaaaacacgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatggtgtgttcgagccctgggattgcaattagattccatgtccactacgtacacggacaagtaaccccgatgtggtcatcagAAGTGTGCAGGATTGGGGACGACCCACCAGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG---------

upper sequence: LOC_Os02g42970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S102_187V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------gtaattagcatgcatgcaagttgatcgaagaatcaaaaaaatcaaagttaggtttgcgattga-------------attga--gcatccaacatgtacaaatattgcagAGAAGTGCAAGATTGG---------CATGGAAGAACAGAATGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCGACGGGCACCCGCACCAACCGGGCCACGGG-
               |    || |   ||   ||||  |||||        | |   |   || | |||| |||||              | |||    || |||  | |      ||  ||| |   |||| ||| ||         ||  ||||| |||| |||||||||||||||||||||||| || || || || ||    || | |||  | || || ||||| |  
gcatgaacatgctcatttgaaggacatatttgagtt--tcgaatttctcccacatagagtttttgttttgggattggtggatatcttgatactgatgatattcaatttttgtggcgatgtcaggggtatgcagGATCGGGGACGTCACCACCGAAGACCAGAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAATATCCTTGCGGGAACCGTGCAAATCGAGCCACCGCC

upper sequence: LOC_Os02g42970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S6_458V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------------------------------------------gtaattagcatgcatgcaagttgatcgaagaatcaaaaaaatcaaagttaggtttgcgattgaattgagcatccaacatgtacaaatattgcagAGAAGTGCAAGATTGGCA---------TGGAAGAACAGAATGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCGACGGGCACCCGCACCAACCGGGCCACGGG
                                                                                   ||  ||  ||  ||     |  ||  |   ||  | | |    |   ||   |    | |||    | ||||    |  | |    |   |||||  |||||  ||||||            ||  | ||||  ||||||||||||||||||||||| ||||| || || || || || | |||| | |||||         
gtaagccaacgaacccacattttgcaggatttcattaacgttggttgaggttagaaaactggaactcgctttagttcgaggaatatataa-atagatatggatatatatatatatatatatatatgagaatactctaagtactgataacaccatctg-tacttgcggcgacatcagAGGTGTGCAGAATTGGCGACGACGCACCCGAGAATCAGAGCGACTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCTACTGGAAACCGCGCAAACCG---------

upper sequence: LOC_Os02g42970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S223_12V6.2 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------gtaattagcatgca----tgcaagttgatcgaagaatcaaaaaaatcaaagttaggtttgcgattgaa-ttgagcatccaacatgta-----caaatattgcagAGAAG---TGCAAGATT--GGC-------ATGGAAGAACAGAATGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCGACGGGCACCCGCACCAACCGGGCCACGGG
                                                                 | |    | |   |    |   |  ||     | || || |  |    | || |  ||||       | || | || | || ||         ||||  ||||    |    ||||| ||   |||       |  ||  | || |  || |  ||||| ||||| | ||| ||||| |||||||||||||||| |||| |||||||         
gtatgcaacaattcatttcagagtattcgtagcatttttcatgttgagggatgtcaatagatttgggacccggaacatagccttaagaactggattgaaaaccacaccacctgatgtgatatttgactccatacttcatcacctaaaattcgggtgttaaatcatgcaacagATCTTTGCAAAATCCAGGCCGACTCAAATGAGAAGCAAACCGATTACTACTTTTTCAGTCGCAAGGACAAGAAGTACCCGACGGGCAACCGCGCCAACCG---------

upper sequence: LOC_Os02g42970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
--gtaattagcatgcatgcaagttgatc-gaagaatcaaaaaaatcaaagttaggtttgcgattgaattgagcat--ccaacatgta-caaatattgcagAGAAGTGCAAGATT---GGCA------TGGAAGAACAGAATGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCGACGGGCACCCGCACCAACCGGGCCACGGG
     || | ||  |      |   | | |||| |     |    ||  || |     |  |  | |||| ||||  | |||   || |    |||||||||   |||||||||   |||         |   | |||||  ||||||||||||| ||||| || ||||| |||||||| || |||| |||| |||||||         
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------

upper sequence: LOC_Os02g42970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
-----gtaattagcatgcatgcaagttgatcgaagaatcaaaaaaatcaaagttagg-----tttgcgattgaattgagcatcc-------aacatgtacaaatattg-----------cagAGAAGTGCAAGATTGGCATGGAAGAACAGAATGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCGACGGGCACCCGCACCAACCGGGCCACGGG
         | | |   || ||   |   |     ||  ||||||| |    || ||     |||||| |  || ||    | |         |||  |  |||   |           ||||   ||||   ||||||   |  || ||| | || |||||||||||||||||||||||||| || |||||||| || ||  | |||||| | ||||| ||
gtaagacggtcatccctcaagcttctcatttcggaaa--aaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG

upper sequence: LOC_Os02g42970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
-----gtaattagcatgcatgcaagttgatcgaagaatcaaaaaaatcaaagttagg-----tttgcgattgaattgagcatcc-------aacatgtacaaatattg-----------cagAGAAGTGCAAGATTGGCATGGAAGAACAGAATGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCGACGGGCACCCGCACCAACCGGGCCACGGG
         | | |   || ||   |   |    |||  ||||||| |    || ||     |||||| |  || ||    | |         |||  |  |||   |           ||||   ||||   ||||||   |  || ||| | || |||||||||||||||||||||||||| || |||||||| || ||  | |||||| | ||||| ||
gtaagacggtcatccctcaagcttctcatttcgggaaa-aaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcaaagttaggtttgcgattgaattgagcatccaacatgtacaaatattgcagAGAAGTGCAAGATTGGCATGGAAGAACAGAATGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCGACGGGCACCCGCACCAACCGGGCCACGGG
                                         tacaaatatt  TA-rich tract