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'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctctatcataccatctcactttctgcacacatttgttttcaaacgtgacatgtctaattagttgtcacatttcagCTTTGCATGGTGCATAAGCTTGGTTATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGCATGTCGCCTTTGTTCCGATTTGATTGGTTTGTCAAGTCCA

Basic information

species Oryza sativa
transcript 13113.m00246
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 14
gtatgctctatcataccatctcactttctgcacacatttgttttcaaacgtgacatgtctaattagttg---tcacatttcagCTTTGCATGGTGCATAAGCTTGGTTATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGCATGTCGCCTTTGTTCCGATTTGATTGGTTTGTCAAGTCCA
||||| | | ||  ||||| | |   | || |   || | |||    || ||||||| ||| | || ||   | ||||| ||||||||||||||||| || ||||| ||||||||||||||||||||||||||||||||||| ||||| || ||||| ||||||||||||||||| |||||||
gtatgtttt-tctcaccatgtta---tgtgtatttatgtatttgagtacatgacatggctactaagctggagttacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA

upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 22
-----------------------------------------gtatgctctatcataccatctcactttctgcacacatttg----ttttcaaacgtgaca-------tgtctaattagttgtcacattt-cagCTTTGCATGGTGCATAAGCTTGGTTATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGCATGTCGCCTTTGTTCCGATTTGATTGGTTTGTCAAGTCCA
                                           ||    | |  | |    ||| || ||       | ||    ||| | |||   |         ||||| | |     | | | || ||| | || ||| | || || ||||| ||||| || ||||||||  |||| || || || || |||||||| ||||| |||||||||||||||||||||||  
gtgtgaattttatttccttttgtttttatttttgcccaaattcatttctttttgttcatgttcagttccttgtttagtctggtgttttccgaacagaattcttgtgttgtctgactttacttaaaacttgcagATATGTATGATTCACAAACTTGGCTATGGTAATTGGGATGAGTTGAAGGCAGCTTTTCGAATGTCGCCCTTGTTTCGATTTGATTGGTTTGTCAAGTCTC

upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 22
-----------------------------------------gtatgctctatcataccatctcactttctgcacacatttg----ttttcaaacgtgacatgtctaattagttgtcacattt--------cagCTTTGCATGGTGCATAAGCTTGGTTATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGCATGTCGCCTTTGTTCCGATTTGATTGGTTTGTCAAGTCCA
                                          |||    | || | |    ||| || ||       | ||    ||| | |||   |    | |  ||  |     || ||        ||| |||| ||| | || || ||||| ||||| || |||||||| ||||| || || || || |||||||| ||||| |||||||||||||||||||||||  
gtgtgaaatttatttccttttgtttttatttttgcccaaatttatttcttttcgttcatgttcagttccttgtttagtctggtgttttccgaacagaattcttgtgttttctgacttcacttaaaacttgcagATTTGTATGATTCACAAACTTGGCTATGGTAATTGGGATGAGCTGAAGGCAGCTTTTCGAATGTCGCCCTTGTTTCGATTTGATTGGTTTGTCAAGTCTC

upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 22
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 22
-----gtatgc-tctatcataccatctc-----actttctgcacacatttgttttcaaacgtgacat--gtctaattagttgtcacatttcagCTTTGCATGGTGCATAAGCTTGGTTATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGCATGTCGCCTTTGTTCCGATTTGATTGGTTTGTCAAGTCCA
       ||   | ||||| ||  | |      | ||  |    |   || | ||| ||  ||| ||    |  || |  |      | |||| | |||||||| ||||| ||||| ||||||||||||||||| || || || || || || |  || || |||||  | ||||| |||||||| || ||| 
gtatgacatctatttatcaaactctttgttgagatttcattgttattgttttattctaatatgatattgacccgatgaacttgtgattatcagATATGCATGGTCCATAAACTTGGGTATGGAAACTGGGATGAGCTAAAGGCAGCGTTTCGGACATCCCCCTTGTTTAGGTTTGACTGGTTTGTAAAATCCC

upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 22
-------------gtatg-ctcta--tcataccatctcactttctgcacacatttgtttt----caaacgtgacatgtctaatta-gttgtcacatttca----gCTTTGCATGGTGCATAAGCTTGGTTATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGCATGTCGCCTTTGTTCCGATTTGATTGGTTTGTCAAGTCCA
               ||  |||||  |  |   ||   | | |  |      |||||||        |  |  |  || || | | |    || | ||||    | | |||||||| || || ||||| ||||| ||||||||||| ||||| || || || ||||  || || ||||| || |||||||||||||| |||||  
gtgagaattgcaatcatctctctagtttgtttgatacaaatgttggtgtgtttttgtttgacgattgatcttccgagtgtattcatgcctccatacttcatgtagATATGCATGGTTCACAAACTTGGATATGGGAACTGGGATGAGCTGAAGGCAGCATTTCGCACTTCTCCCTTGTTTCGTTTTGATTGGTTTGTAAAGTCTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 69 (upstream exon), 67 (downstream exon)
Score: 17

GAAGAAGTTAGACCGCTATAAGAATCCATGGTTAGAGTTGAAAATCCAGTATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATGgtatgctcta ... cacatttcagCTTTGCATGGTGCATAAGCTTGGTTATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGCATGTCGCCTTTGTTCCGATTTGATTGGTTTGTCAAGTCCA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgcacacatttgttttcaaacgtgacatgtctaattagttgtcacatttcagCTTTGCATGGTGCATAAGCTTGGTTATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGCATGTCGCCTTTGTTCCGATTTGATTGGTTTGTCAAGTCCA
                               gtctaat  putative branch site (score: 17)
          atttgtttt  TA-rich tract