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

gtagtttcgtcttcctttttaatcaagtgcaaagtgtgataattgttctaacagctatctatggcataatcttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCTCCTGGGAAGGCCACCATCC

Basic information

species Oryza sativa
transcript LOC_Os09g36180.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g36180.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G386971_T01 (Zea mays), 3'ss of exon 7
gtagttt-cgtcttccttt------ttaatcaagtgcaaagtgtgataattgttctaacagctatctatggcataatcttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCTCCTGGGAAGGCCACCATCC
||| ||| ||| | | |||      ||| |||| ||||       |      ||||||  |  || | ||||||    ||||||||| || ||||| ||||||||||||||||||||||| ||||| ||||||||||||||||||||||||||| |||||||||| ||||| |||||||||||||
gtattttgcgtgtacttttagtcaattattcaattgcactccactaagtagtttctaatggtgatgtttggcatgtctttttcagGAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCCACCATCC

upper sequence: LOC_Os09g36180.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G379577_T01 (Zea mays), 3'ss of exon 7
gtagtttcgtcttcctttttaatcaagtgcaaagtgtgat-------aattgttc-taacagctatctatggcataatcttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCTCCTGGGAAGGCCACCATCC
||| ||||   | |  ||||| |||| |    | |   ||       | | |||| |||||   || | ||| ||   |||||||| | || ||||| ||||||||||||||||||||||| ||||| ||||||||||||||||||||||||||| |||||||||| ||||| ||||| |||||||
gtattttc-catgcacttttagtcaattattcaattgcattcctcaaagtagttcctaacattgatgtttggaatgtccttttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC

upper sequence: LOC_Os09g36180.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA09G40260.1 (Glycine max), 3'ss of exon 8
--------------------------------------------------------------------------------------------------------------gtagtttcgtc--ttcctttttaatcaagtgcaaagtgtgataa----ttgttctaacagc----tatctatggcataatcttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCTCCTGGGAAGGCCACCATCC
                                                                                                               | ||||   |  | | |   | |   |||  | | | | || |    |||   | |        | | | || | | | | || ||||| |||  ||||||||| || || ||||| ||||||||  | || ||||||||||||||||||||||||||| |||| |||||||| || || || ||| 
gtgacttaaacagtcttttaccataccagtgtgtatgtgcatgtctatatagatattcttttatatagatgatgaataatttgtgcttgcactgtacaacccggacatattttgtttgtgcagtgcatccctgactcagtaaataatataattaaactttgccttcattatcttatgtttgtgtcttcaacattgcagGATCCTTCGAAGCATGTGTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTTTGTTGAATCCTCCTGGAAAAGCTACAATCA

upper sequence: LOC_Os09g36180.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA07G08910.1 (Glycine max), 3'ss of exon 5
--------------------gtagtttcgtcttcctttttaatcaagtgcaaagtgtgataattgttctaacagctatcta--tggcataatcttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCTCCTGGGAAGGCCACCATCC
                    ||      || |   |  || |  || |   |  | | | |   |  || | | || | |   || | | | | || ||||| |||   ||||||||||| || ||||| || |||||  | || |||||||||||||||||||||||| |  | ||||||||||  || || || ||||
gcaccaaaaatatcgtgcatgtgaaagtgtatctatgatttagtaaattatacttttaaaaccaggcctcataactttgttattgtcttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC

upper sequence: LOC_Os09g36180.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA18G45750.1 (Glycine max), 3'ss of exon 7
----------------------------------------------------------------------------------------------------------------gtagtttcgtcttcctttttaatcaagtgcaaagtgtgat--aattgttctaacagctatctatggcataatctttt-------cagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCTCCTGGGAAGGCCACCATCC
                                                                                                                 |  || | | | | |   | |  || |  | | | | ||  || | | |   ||      ||||      ||||          |||| |||  ||||||||| || || ||||| ||||||||  | || ||||||||||||||||||||||||||| |||| |||||||| || || || ||| 
gtgacttggactgtctttttccataccagtgtgtgtgtacatgtctgtatagtgaatttttttttatagatgatgaataatttgtgcttgcactgtacaacccggacatagtttgtttgcttgtgcatccctgacaaaataaataatataattaaactttgccttcattatcttatgttcgtgtcttccaacgttgtagGATCCTTCGAAGCATGTGTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTTTGTTGAATCCTCCTGGAAAAGCTACAATCA

upper sequence: LOC_Os09g36180.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA03G02250.1 (Glycine max), 3'ss of exon 13
-------------------------------------------------------------------------------------------------------------gtagtttcgtcttcctttttaatcaagtgcaaagtgtgataatt-gttctaacagct--atctatggcataatcttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCTCCTGGGAAGGCCACCATCC
                                                                                                             ||      || |   |  || |  || |  | | | | | ||   |  || | | ||   | | || | | |   || ||||| ||   |||| ||||||| || ||||| ||||||||  | || ||||||||||||| |||||||||| |  | ||||||||||| || || || ||||
gtgacttgggctgtctttttaaccataccagtatttgtgtgcaagttcattgtttccttttatagattgcaaataagggtgccttgaccatggtcaacatatcgtgcatgtgaaagtgtatctatgatttagtaaat-tatattattaaaaccaggcctcataacttagtttctgtcttcaatgttgcagGATCCATCGAAGAATGTTTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAGCATGTGGTTTCTTTTAAACCCTCCTGGAAAAGCTACAATCC

upper sequence: LOC_Os09g36180.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G46480.1 (Arabidopsis thaliana), 3'ss of exon 3
gtagtttcgtcttcctttttaatcaagtgcaaagtgtgataattgttctaacagctatctatggcataatcttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCTCCTGGGAAGGCCACCATCC
||| |       ||| |  ||||       | | |  |    ||   || |||     |||  |  |    ||  ||||| |||   | |||||||||||| ||||||||||||||| | ||||||||||| ||||  ||||||||| || |||||||||||||  | || |||||||
gtaatgat-caatccctagtaattgttgcaagaataagtgctttaaacttacaag-gcctactgggtttatttggcagGATCCTTCAAGGCATGTTTTCCACCTTGTGACTGATAAGCTCAACTTTGGAGCAATGAGTATGTGGTTTCTGTTGAACCCTCCTGGAGAAGCGACCATCC

upper sequence: LOC_Os09g36180.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv15s0048g01300.t01 (Vitis vinifera), 3'ss of exon 8
----------------gtagtttcgtcttcctttttaatcaagtgcaaagtgtgataattgttct--aacagctatctatggcataatctt----ttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCTCCTGGGAAGGCCACCATCC
                |   |||  |          ||    |    |  | || |  |  || |  |    |||  | ||  |  | | |    | ||||| || || || ||||| |||||||| || ||||||||| |||| |||||||||||||| ||||||||| || ||||||| || || || || || ||||
tttggataagcgaaaggggatttgttaggaaagcacaaaagggcatcacatatgttcttcctttttcattcactaagtttgctaataccctcgattgcagGAACCAGAAAAACATGTATTCCATCTGGTTACTGATAAGCTGAATTTTGGAGCCATGAATATGTGGTTTCTGTTGAACCCCCCAGGAAAAGCAACTATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagtgcaaagtgtgataattgttctaacagctatctatggcataatcttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCTCCTGGGAAGGCCACCATCC
                      ttctaac  putative branch site (score: 1)
                                              tcttttc  putative PPT
                                          ataatctttt  TA-rich tract