Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttcttaccataagaatttttttacgtgatcaattgtatgctgatgcaagtgcgctaagatgagatagttcacttgcattcagATGTCAGATCCTCTTACTGCTCTGATGCATGCTGTTCAAGTGATGAATCTTCTCAAGACATTGATTCTCAAGACGCTTAGAGAACGTGAGCATGATGAAA

Basic information

species Oryza sativa
transcript LOC_Os07g22580.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g22580.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G143253_T01 (Zea mays), 3'ss of exon 4
gtaattt-ttcttaccataagaatttttttacgtgatcaa--ttgtatgctgatgcaagtgcgctaagatgag----atagttcacttgcattcagATGTCAGATCCTCTTACTGCTCTGATGCATGCTGTTCAAGTGATGAATCTTCTCAAGACATTGATTCTCAAGACGCTTAGAGAACGTGAGCATGATGAAA
||| ||  ||||| ||  |||   | |   || |  || |  |||| |||||   ||  || ||||| | ||       | ||  | | ||| |||||||| |||||||| || || ||||||||||||||||||||||||||  | ||||| || || |||||||| || ||| | ||||| ||| |||||||  
gtatttccttcttgcc--aagtcctctaacacatcgtcgaccttgtttgctgtgacacttgtgctaacaagaacatcgaaattttcctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG

upper sequence: LOC_Os07g22580.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G02720.1 (Glycine max), 3'ss of exon 3
--gtaatttttcttaccata------agaatttttttacgtgatcaattgtatgctgatgcaagtgcgctaagatgagatagttcacttgcatt----cagATGTCAGATCCTCTTACTGCTCTGATGCATGCTGTTCAAGTGATGAATCTTCTCAAGACATTGATTCTCAAGACGCTTAGAGAACGTGAGCATGATGAAA
     ||||| |||||  ||      |||  || |  || |||  || | | |   | || || ||  |||     |  |  |     |    |    |||||||| |||||||| || || ||||||||||| ||||||||||||||  | ||||||||| | ||  | ||||| ||||||||||  || ||    | ||
gccatattttgcttacagtaggctatagatcttatgcacatgaa-aactatgtatagttgaaaatggtctattgctaattcatctgtgtctcctggaacagATGTCTGATCCTCTAACAGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTCATCATGAAGACACTTAGAGAACACGAACAAACAGCAA

upper sequence: LOC_Os07g22580.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G17070.1 (Glycine max), 3'ss of exon 3
gtaatttttcttaccataag-------aatttt-tttacgtgatcaat-tgtatgctgatgcaag---tgcgctaagatgagatagttcacttgcattcagATGTCAGATCCTCTTACTGCTCTGATGCATGCTGTTCAAGTGATGAATCTTCTCAAGACATTGATTCTCAAGACGCTTAGAGAACGTGAGCATGATGAAA
    |||| |||||  || |       | | || || || |||  | |  | ||||||    | |   ||     |  | |  |    | | || |  |||||||| |||||||| ||||| ||||||||||| ||||||||||||||  | ||||||||| | ||  | ||||| ||||||||||| ||  |    | ||
catgttttgcttacactaggctatgctactcttattcacatgagaactacgaatgctggaaaatggtctgtttctaattcatctttgcctcctggaa-cagATGTCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTTATCATGAAGACACTTAGAGAACGCGAAGAAACAGCAA

upper sequence: LOC_Os07g22580.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G36630.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------gtaatt-tttcttaccataagaatttttttacgtgatcaattgtatgctgatg------caagtgcgctaagatgagatagttcacttgcatt------cagATGTCAGATCCTCTTACTGCTCTGATGCATGCTGTTCAAGTGATGAATCTTCTCAAGACATTGATTCTCAAGACGCTTAGAGAACGTGAGCATGATGAAA
                                                                ||  ||  || ||||||| || || | || |  |||| |    |||||  |        | |||    |    | | ||| || | ||   |       |||||||| ||||| || ||||||||||||||||| || |||||||||||| | || |||||  | ||  | ||||| ||||||||||| ||  |    |   
gtatgttacatgtatgcttaatgagctcatattttaattatacatgtaacatctttactatgacgttgttacttgttaccattagcatgtattcatatgatgataactatgcaaactggaaatctagtattttttattcacatattttatttttctcttgaaacagATGTCTGATCCACTAACTGCTCTGATGCATGCGGTCCAAGTGATGAATTTACTAAAGACCCTAATATTGAAGACACTTAGAGAACGCGAAGAAACAGCTG

upper sequence: LOC_Os07g22580.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatttttcttaccataagaatttttttacgtgatcaattgtatgctgatgcaagtgcgctaagatgagatagtt-cacttgca---ttcagATGTCAGATCCTCTTACTGCTCTGATGCATGCTGTTCAAGTGATGAATCTTCTCAAGACATTGATTCTCAAGACGCTTAGAGAACGTGAGCATGATGAAA
          | |  | ||   |    ||   | |   | |         ||        |||| ||  |||  || || |  |    |  ||||| |||||||  | || ||||| |||||||||||||||||||||||  | || |||||  | ||    ||||| ||    ||||| ||  |  |||  |
---------gtaaaaacaaagttaacctttgttcaatgaataagaatcactgagtagttactaacatttgattcttgcattctctaactgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA

upper sequence: LOC_Os07g22580.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
gtaatttttcttaccataagaatttttttacgtgatcaattgtatgctgatgcaagtgcgctaagatgagatagttc---acttgcattca---gATGTCAGATCCTCTTACTGCTCTGATGCATGCTGTTCAAGTGATGAATCTTCTCAAGACATTGATTCTCAAGACGCTTAGAGAACGTGAGCATGATGAAA
||   | ||   | | | | ||||| ||    |    |||  | || |      | | |  |||   ||  |  ||      |||  ||||   |||||| |||||  | || |||||||||||||||||||||||||||||  | || |||||  ||||    || || || || ||||| ||  |        
gttgatattaa-atcttgaaaatttcttgttttagctaatgctttggtccatggatttcaataaatagaactccttttttgtttgatttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG

upper sequence: LOC_Os07g22580.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S107_15V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------------------------------------------------gta-atttttcttaccataagaatttttttacgtgatcaattgta-----tgctgatgcaagtg--cgctaagatgagatagttcacttgcatt-cagATGTCAGATCCTCTTACTGCTCTGATGCATGCTGTTCAAGTGATGAATCTTCTCAAGACATTGATTCTCAAGACGCTTAGAGAACGTGAGCATGATGAAA
                                                                                               | | ||| ||    ||   |   |  |||   || |     |||      || ||| | | ||   | ||  ||| |  |   |  |||||  | ||||||   ||||| || || |||||||||||||| ||||||||||||||  |  | || || ||||||||    ||  | |  || ||  ||  |  |    
gtatagagcacctcttcggtggtctctttcttttgaaactagtttagagctaaaactgtgtagcgtgttgtctcccgtgttttctcatgatctttgcacattatttcagcctcgaaggtcgtttgttgttagttggtgttcgatctgttgacgaaggtcatctctttgataatttgagtttcttgccctgcagATGGTTGATCCGCTAACGGCTCTGATGCATGCCGTTCAAGTGATGAACTTGTTGAAAACTTTGATTCTACGCACATTGAAGGACCGGAAGGCTACTTTGC

upper sequence: LOC_Os07g22580.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S60_256V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------------------------------------------------gtaatttttcttaccataagaatttttt-tacgtgatcaattgtatgctgatgcaagtgcgctaa--gatgagatag-ttcacttgcattcagATGTCAGATCCTCTTACTGCTCTGATGCATGCTGTTCAAGTGATGAATCTTCTCAAGACATTGATTCTCAAGACGCTTAGAGAACGTGAGCATGATGAAA
                                                                                                     ||  |   | | | | || | |||   | |   || |   |    || ||  | | |||    |     ||| || | |||| |  | |||||||| | ||||| || || ||||||||||||||||||||||| |||||  | ||||| ||  |||||||    || || |  || ||  ||     |    
gtatagtgttgtttctacgcttttcacccagagaagctgatgaccattacaagatcagactcgtagagatttcactacagatgctgtcttcgacgtttcatgtgctgaatttgaacgtaggtattccgtgtttatggtgtttcaattgttgtagaatgtgtaacatttattgacattgcttcattatccttcagATGGCTGATCCACTGACAGCTCTGATGCATGCTGTTCAAGTCATGAACTTGCTCAAAACTCTGATTCTTCGCACACTGAAGGACCGAAAGGCCACTTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaattgtatgctgatgcaagtgcgctaagatgagatagttcacttgcattcagATGTCAGATCCTCTTACTGCTCTGATGCATGCTGTTCAAGTGATGAATCTTCTCAAGACATTGATTCTCAAGACGCTTAGAGAACGTGAGCATGATGAAA
          tgctgat  putative branch site (score: 3)
                                        ttcactt  putative PPT