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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttgttgttatcttctacccattcagatgtatggggcaaagtccctaaatgtcacttcatctctgtaaatagGGAATCTGAACCCAATTCCTGGGAGGACACCATGAAAGATGAGCTGGACCGTGATAAATATCCCCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAT

Basic information

species Zea mays
transcript GRMZM2G066485_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g29050.2 (Oryza sativa), 3'ss of exon 11
---------gtattttgttgttatcttctacccattcagatgtatggggcaaagtccctaaatgtcacttcatct-ctgtaaata-gGGAATCTGAACCCAATTCCTGGGAGGACACCATGAAAGATGAGCTGGACCGTGATAAATATCCCCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAT
         |||||| |||  |   |  ||   ||  ||   |||    |||| |      |  | | ||   || ||||| ||| |||||||||| || ||||||||||||||||| ||||||||||||||||||||    |||||||| ||||||||||||||||||||||||||||||||||| 
gtaactatggtatttcgtttatga-tggtatttatgtaggattattcc-caaattattcttacctgagttttcctgctgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC

upper sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 10
----------------------gtattttgttgttatcttctacccattcagatgtatgggg--caaagtccctaaatgtcacttcatctctgtaaatagGGAATCTGAACCCAATTCCTGGGAGGACACCATGAAAGATGAGCTGGACCGTGATAAATATCCCCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAT
                      ||  ||  || |||  |  |        || | | |   |  ||| |    |||  |   | |  ||  | |  | || ||||||||||| ||||| ||||| || || |||||||||||  | || ||||| |||||||| || |||||||||||||||||||| ||||| || |  
cactttgaatgtgttaagatatgtcattcattattaattgatcatagactagctctttcctgttcaacgatagtaatagattcattttcaattttgacagAGAATCTGAACCAAATTCATGGGAAGATACAATGAAAGATGAATTAGAACGTGAAAAATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGG

upper sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 10
-------------gtattttgttgttatcttctacccattcag-atgtatggggcaaagtccctaaatgtcact-------tcatctctg---taaatagGGAATCTGAACCCAATTCCTGGGAGGACACCATGAAAGATGAGCTGGACCGTGATAAATATCCCCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAT
             || ||  | ||| ||     |   ||| |  ||  |  |  |       || || || | |       |||| |      |  | || ||||||||||| ||||| ||||| || || |||||||||||  | || ||||| |||||||| || |||||||||||||||||||| ||||| || |  
ttgcactttgaatgtgttaagatgtcattcatcattaattaatcatagacagctctttcctgctgaacgttagtaatatattcattttcaattttgacagAGAATCTGAACCTAATTCATGGGAAGATACAATGAAAGATGAATTAGAACGTGAAAAATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGG

upper sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA20G38200.1 (Glycine max), 3'ss of exon 11
------------------------gtattttgttgttatcttctacccattcagatgtatggggcaaagtccctaaatgtcacttcatctctgtaaatagGGAATCTGAACCCAATTCCTGGGAGGACACCATGAAAGATGAGCTGGACCGTGATAAATATCCCCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAT
                         |    | ||| |      |   | ||   | ||     | ||  |     ||| |    |  | |  ||  |||| |||||||| || ||||| ||||| |||||||||||||||||  |||| ||  | || |||||||| ||||| ||||| ||||| || |||||||| |  
cattacaattagccgtgttggagccttcactattgctgatgagtctgcttttctaagttcttagtaatattatataatttgtaattttgttggttgatagAGAATCTGAGCCAAATTCATGGGAAGACACCATGAAAGATGAATTGGATCGCAAGAAGTATCCCCGTATGCCATGGCACGATGTCCATTGTGCTCTTTGG

upper sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------------gtattttgttgttatcttctacccattcagatgtatggggcaaagtccctaaatgtcacttcatctctgtaaatagGGAATCTGAACCCAATTCCTGGGAGGACACCATGAAAGATGAGCTGGACCGTGATAAATATCCCCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAT
                                 ||  |  |||  |  || |   || || |     |    || | |   ||| |   | |  || |        |||||||||||||| ||||| ||||| || || |||||||||||  |||| ||||  |||||||| || ||||| |||||||| || || ||||| || |  
gtgtgagaacattgacaatagtttcttcttttctaagtaattgcaagtttgttttcactctggctcttt---cacattggataacttgtaatgaattttcaatttcagGGAATCTGAACCAAATTCTTGGGAAGATACAATGAAAGATGAATTGGATCGTGGAAAATATCCTCGTATGCCATGGCATGACGTCCATTGTGCCCTATGG

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 4 RNA-Seq libraries.


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 28

GAGGTCTTGATCTGTGCTTTGGTCGCTACGATAGTCCTGAGCACAAAGTCGCTGATTCTCCTCCAGAGATGTGGCCAGGAAAGGACTACTACAATCCCAGgtattttgtt ... ctgtaaatagGGAATCTGAACCCAATTCCTGGGAGGACACCATGAAAGATGAGCTGGACCGTGATAAATATCCCCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAT


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 66

GAGGTCTTGATCTGTGCTTTGGTCGCTACGATAGTCCTGAGCACAAAGTCGCTGATTCTCCTCCAGAGATGTGGCCAGGAAAGGACTACTACAATCCCAGgtattttgtt ... ctgtaaatagGGAATCTGAACCCAATTCCTGGGAGGACACCATGAAAGATGAGCTGGACCGTGATAAATATCCCCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAT


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 54

GAGGTCTTGATCTGTGCTTTGGTCGCTACGATAGTCCTGAGCACAAAGTCGCTGATTCTCCTCCAGAGATGTGGCCAGGAAAGGACTACTACAATCCCAGgtattttgtt ... ctgtaaatagGGAATCTGAACCCAATTCCTGGGAGGACACCATGAAAGATGAGCTGGACCGTGATAAATATCCCCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAT


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 90

GAGGTCTTGATCTGTGCTTTGGTCGCTACGATAGTCCTGAGCACAAAGTCGCTGATTCTCCTCCAGAGATGTGGCCAGGAAAGGACTACTACAATCCCAGgtattttgtt ... ctgtaaatagGGAATCTGAACCCAATTCCTGGGAGGACACCATGAAAGATGAGCTGGACCGTGATAAATATCCCCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccattcagatgtatggggcaaagtccctaaatgtcacttcatctctgtaaatagGGAATCTGAACCCAATTCCTGGGAGGACACCATGAAAGATGAGCTGGACCGTGATAAATATCCCCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAT
                         ccctaaa  putative branch site (score: 90)
                                     cttcatctct  putative PPT
                                              tgtaaata  TA-rich tract