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

...ttttgtggcaagagctttggggagaacattatttgtataataatatttcgtttgtgttgatgttagctaatagactaagtgtttgttgaacttctgccagCTTATATATCAGGTTGGTCAAAAAAGAGGTCGCCTAACGATGGACGAAGATGATGATGAGCAGCCAAAAAAGAAGATTAGAATGGGCATGCCTGCAACTC

Basic information

species Oryza sativa
transcript LOC_Os05g11140.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 10
----------------------------------------------------------------ttttgtggcaagagctttggggagaacattatttgtataataatatttc-gtttgtgttgat--gt-tagctaatagactaagtgtttgttgaacttctgccagCTTATATATCAGGTTGGTCAAAAAAGAGGTCGCCTAACGATGGACGAAGATGATGATGAGCAGCCAAAAAAGAAGATTAGAATGGGCATGCCTGCAACTC
                                                                ||| ||   |||   | ||||       |||||||||  |  | |  || |  |    ||||  || ||| || ||   || |  ||| | ||  |||| ||||||| ||| |||||| || || || ||||||||||| |||||||| |||||||||||||||||||| |||||||||||| | ||||| |||||||| || |
gtattgttctatccaaccttgttgctccttgttcttgttaactaaagcttgcttccagccattgtttggtactaaggcttctgggccattggttatttgtaccagtacacatctgcatacaatgattggtatagatactaatatatgcttttat-gattttctaccagCTTGTATTTCAGGTAGGCCAGAAGAGAGGTCGCCTTACGATGGAGGAAGATGATGATGAGCAGCCCAAAAAGAAGATTCGGATGGGAATGCCTGCGACCC

upper sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 10
ttttgtggcaagagctttggggagaacattatttgtataataatatttcgtttgtgttgatgttagctaatagactaagtgtttgttgaacttctgcc----agCTTATATATCAGGTTGGTCAAAAAAGAGGTCGCCTAACGATGGACGAAGATGATGATGAGCAGCCAAAAAAGAAGATTAGAATGGGCATGCCTGCAACTC
    ||    |   || |    |    |  |||||  |  | ||   |    | | |  |   |  ||    ||||     ||| |||   |  |       ||||||||| ||||||||| || || || || ||  | || || || |||||||||||||| || ||||| |||||| || ||||||| |||||||| || |
----gtacttaattctattattattttaaaatttgctt--ttattgcttacatatttaaagtctgactg--tgactgccctttttttgggttattattctgtagCTTATATGTCAGGTTGGACATAAGAGGGGGCGATTGACCATAGAAGAAGATGATGATGAACAACCAAATAAGAAGGTTCGAATGGGAATGCCTGCTACAC

upper sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 10
ttttgtggcaagagctttggggagaacattatttgtataataatatttcgtttgtgttgatgttagctaatagactaagtgtttgttgaacttctgccagCTTATATATCAGGTTGGTCAAAAAAGAGGTCGCCTAACGATGGACGAAGATGATGATGAGCAGCCAAAAAAGAAGATTAGAATGGGCATGCCTGCAACTC
 |   |      |   ||      ||  ||  || |||     ||  |  ||   ||   ||   | || |   ||   | |  |||    |||||  ||||||||| ||||||||| || || || || ||  | || || || |||||||||||||| || ||||| |||||| || ||||||| |||||||| || |
gtacttaattctattattattttaaaatttgcttttattgct-tacatatttaaagtc--tgactgttactgccctttttttgggttattattctgt-agCTTATATGTCAGGTTGGACATAAGAGGGGGCGATTGACCATAGAAGAAGATGATGATGAACAACCAAATAAGAAGGTTCGAATGGGAATGCCTGCTACAC

upper sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 10
---ttttgtggcaagagctttggggagaacattatttgtataataatatttcgtttgtgttgatgttagctaatagactaagtgtttgttgaacttctgccagCTTATATATCAGGTTGGTCAAAAAAGAGGTCGCCTAACGATGGACGAAGATGATGATGAGCAGCCAAAAAAGAAGATTAGAATGGGCATGCCTGCAACTC
    ||  ||  || |    |   ||      | ||| | |  | | || | |   || |   ||||      | | |   || |  | |    |||||  ||||||||| ||||||||| || || || || ||  | || || || |||||||||||||| || ||||| |||||| || ||||||| |||||||| || |
gtacttaatgctaatattactttagaatttgctttttat-tgcttacatattgaaagtctgactgttg-----ttgcccttgtttgggctattattctgt-agCTTATATGTCAGGTTGGACATAAGAGGGGGCGATTGACCATAGAAGAAGATGATGATGAACAACCAAATAAGAAGGTTCGAATGGGAATGCCTGCTACAC

upper sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 10
ttttgtggcaagagctttggggagaacattatttgtataataatatttcgtttgtgttgatgttagctaatagactaagtgtttgttgaacttctgcca-gCTTATATATCAGGTTGGTCAAAAAAGAGGTCGCCTAACGATGGACGAAGATGATGATGAGCAGCCAAAAAAGAAGATTAGAATGGGCATGCCTGCAACTC
    ||  | |    | |        |  || | | |||  ||| | |  |     |||   || |  | |  |   |   | | || | ||  ||  | |||||||||||||||||| || || ||||| || || || ||||| || |||||||||||||| ||||| |||||| |  ||||||| ||||||||||| |
----gtacccatttatgtttatctgtctgtact-gaatatgaatttcttttcacatttggctttgg--agtgcatctaacatgtatttacctattgtgaagCTTATATATCAGGTTGGACATAAGAGAGGACGACTGACAATGGAGGAGGATGATGATGAGCAACCAAAGAAGAAGGTCCGAATGGGAATGCCTGCAACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgtttgtgttgatgttagctaatagactaagtgtttgttgaacttctgccagCTTATATATCAGGTTGGTCAAAAAAGAGGTCGCCTAACGATGGACGAAGATGATGATGAGCAGCCAAAAAAGAAGATTAGAATGGGCATGCCTGCAACTC
                   agctaat  putative branch site (score: 3)
                                             cttctgcc  putative PPT
                      taataga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgtggcaagagctttggggagaacattatttgtataataatatttcgtttgtgttgatgttagctaatagactaagtgtttgttgaacttctgccagCTTATATATCAGGTTGGTCAAAAAAGAGGTCGCCTAACGATGGACGAAGATGATGATGAGCAGCCAAAAAAGAAGATTAGAATGGGCATGCCTGCAACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG