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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatttagcggaagtttcaaatgaacagtgaactgtagactggacattgaattgctgttctttgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA

Basic information

species Oryza sativa
transcript LOC_Os08g33830.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 1
--------ttgatttagcggaagtttcaaatgaacagtgaactgtagactggacattgaattgctgttctttgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA
         ||   | || ||  ||| |  |  | | |    |    |        | | |   ||||| ||      || || |    | ||  | |   |||||||||||||||||||||||||||||||||||| || ||||||||||| ||||||||||||||||||||||| || |||||||| |||||||| || |||||||
actgtatgctgcacttgcagagtttttagttctatatta---ttcgaatctcctgcttagtcagtgttcctta-----cagttgtcccttcaacatgcacattttcagGCAGATCAAAACCAGGCAATTTCAATGGTGTCCTATTATGCTTCATCTTCAGAACCTGCTCAAGTTCGCGGTAAAACTGTCTATATCCAATATTCAAACA

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G082174_T03 (Zea mays), 3'ss of exon 1
----ttgatttagcggaagtttcaaatgaacagtgaactgtagactggacattgaattgctgttctttgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA----
     |||  | || ||  ||| |  |    | |    |    | |      | | |   ||||||||  |  |  |        | ||  | |   |||||||||||||||||||||||||||||||||||| || ||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| || |||||||    
tatgctgaacttgcagaccttttagttttgtatta---ttcgaatttcctgcttagtcaatgttctttactgttttccct-----tcaacatgctcattttcaggcagATCAAAACCAGGCAATTTCAATGGTGTCCTATTATGCTTCATCTTCAGAACCTGCTCAAGTTCGTGGTAAAACTGTATATATCCAATATTCAAACAGGCA

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G082174_T02 (Zea mays), 3'ss of exon 1
--------ttgatttagcggaagtttcaaatgaacagtgaactgtagactggacattgaattgctgttctttgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA
         |||  | || ||  ||| |  |    | |    |    | |      | | |   ||||||||  |  |  |        | ||  | |   |||||||||||||||||||||||||||||||||||| || ||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| || |||||||
actatatgctgaacttgcagaccttttagttttgtatta---ttcgaatttcctgcttagtcaatgttctttactgttttccct-----tcaacatgctcattttcagGCAGATCAAAACCAGGCAATTTCAATGGTGTCCTATTATGCTTCATCTTCAGAACCTGCTCAAGTTCGTGGTAAAACTGTATATATCCAATATTCAAACA

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA18G49580.1 (Glycine max), 3'ss of exon 1
-ttgatttagcggaagtttcaaatgaacagtgaactgtagactggacattgaattgctgttctttgttcctcacttatattataaatgtacctttttt--cagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA-
  ||| | |     ||| ||  | ||   ||   || || | |  |   |     |   || |||  |  |   |||  |   || | ||| |  |||  ||||  |||| ||| || || ||||| |||||||||||||||||||| ||||||||||| |||   |||||||| |||||||| || || ||||| || || | 
agtgactgatt---agtgtctgaggatgtgttttct-tatatttaatgatacccggtcctttttttatgattttttaactctcaagtatacatgctttaccaggTGGATCTAAATCAAGCCATTTCGATGGTTTCATATTATGCTTCATCTTCAGAACCAGCTATGGTTCGTGGTAAAACTGTTTACATTCAGTATTCTAATAG

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 1
ttgatttagcggaagtttcaa-atgaacagtgaactgtagactggacattgaattgctgttctttgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA
 ||| |   ||   ||   |  |||     |    | |    ||     ||  |   | || ||| ||  |   |||  | |   ||  |   |||  ||||| |||| ||| || || ||||| |||||||||||||||||||| ||||||||||| |||   |||||||| |||||||| || || ||||| || || |
gtgact-gccgagcgtccgaggatgtgttttcttatatttgatgatacctggttctttttttttttttttttttttaactcaattatacatgctttgccagGCGGATCTAAATCAAGCCATTTCGATGGTTTCATATTATGCTTCATCTTCAGAACCAGCTATGGTTCGTGGTAAAACTGTTTACATTCAGTATTCTAATA

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G01150.2 (Arabidopsis thaliana), 3'ss of exon 1
ttgatttagcggaagtttcaaatgaacagtgaactgtagactggacattgaattgctgttctt-tgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA
   ||  |   |   | |||| |         |   | |      | |  |  |   ||| |   | |    | | ||     |    |    |||| ||||| ||    || || || || ||||||||||| ||||||||||| |||||||| || || ||  ||||||| |||||||| ||||| |||||||| ||  
-gtatcgaataggtttctcaagttttatagctatgatggttgactcttcaagctttcgttttggcgatttctattgatgaaccattcatttgattttacagGCTGACTTGAATCAAGCTATATCAATGGTTTCGTATTATGCTTCATCTTCAGAGCCCGCACAGATTCGTGGGAAAACTGTCTATATTCAGTACTCTAATC

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv14s0108g01030.t01 (Vitis vinifera), 3'ss of exon 1
--ttgatttag--cggaagtttcaaatgaacagtgaactgtagactggacattgaattgctgttctttgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA
   ||| || |  | |   | | ||||  |    ||  || ||  |   | ||   |   || |  | | |     || | |  | |  | ||  | ||| |||   || |  || ||||| ||||| |||||||||||||||||||| ||||| |||||||| || |||||||| || ||||| |||||||| ||||| ||||
tggtgacttggatccgggttattaaatttatttcgagatgcagtttt--ctttttctctttggtggtggctatatgctgaca--aaaggtatatttctttgcagTTGGACCTTAATCAGGCCATTTCTATGGTTTCATATTATGCTTCATCTTCGGAACCTGCACAGGTTCGTGGTAAGACTGTGTATATCCAATACTCTAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgaattgctgttctttgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA
                     tcctcac  putative branch site (score: 2)
                                          taccttttttc  putative PPT
                            ttatattataaatgta  TA-rich tract