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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagctcatattctgatatcacctcaagttctcaagtacattcattatgttctcgcagcatatagattggattcataatgtcaatgttttgcatctgcagTGTATTACCTTCAGGGCTGTCGTGTCTTCAGAGAGACACACCCTGTTTTCTTGGCTCTCCACAAT

Basic information

species Zea mays
transcript GRMZM2G155837_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g52630.1 (Oryza sativa), 3'ss of exon 13
-taagctcatattctgatatcacctcaagttctcaagtacattcattatgttctcgcagcatatagattggattcataatgtcaatgttttgcatctgcagTGTATTACCTTCAGGGCTGTCGTGTCTTCAGAGAGACACACCCTGTTTTCTTGGCTCTCCACAAT
 |     |||||||  || ||  ||||    |||||| | |      |  ||||| |||| | ||  || |||  | |||||  ||||||| |||||| ||||| |||||||||||||||  ||| ||||||||| |||| ||||| |||||||| |||||||| |
gtgcatccatattcgaatttcttctcacaaactcaagcataaat-ccagattctctcagcttctaatttcgatcgaaaatgttgatgtttttcatctgtagTGTCTTACCTTCAGGGCTGGAGTGCCTTCAGAGAAACACGCCCTGCTTTCTTGGTTCTCCACATT

upper sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g52600.1 (Oryza sativa), 3'ss of exon 15
-taagctcatattc-tgatatcacctcaagttctcaagtacattcattatgttctcgcagcatatagattggattcataatgtcaatgttttgcatctgcagTGTATTACCTTCAGGGCTGTCGTGTCTTCAGAGAGACACACCCTGTTTTCTTGGCTCTCCACAAT
 |  |  || |||  | || || | |||||| |||||| | | | |||| ||||||  ||| | || ||||||| || |||||   ||||||||||||||||| | ||||||||||||||  | || ||||| ||| | || || ||||||||||| |||||||| |
gtgcgtccacatttgtaatttctcatcaagtactcaagcataattattaggttctccaagcttcta-attggatgcaaaatgttggtgttttgcatctgcagTATCTTACCTTCAGGGCTTGCATGCCTTCAAAGAAATACGCCATGTTTTCTTGGTTCTCCACAGT

upper sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g52614.1 (Oryza sativa), 3'ss of exon 11
taagctcatatt-ctgatatcacctcaagttctcaagtacattcattatgttctcgcagcatatagattggattcataatgtcaatgttttgcatctgcagTGTATTACCTTCAGGGCTGTCGTGTCTTCAGAGAGACACACCCTGTTTTCTTGGCTCTCCACAAT
|  || |||||| ||||| || |  ||||  |||||| | | | | || |||||| |||| | || ||| |||||| | |||  ||| | |||| ||||||| | ||||||||||||||| | || ||||||||| | ||| |||  |||||||| |||||||| |
tgcgcccatatttctgatttctcaacaagaactcaagcataattaataggttctctcagcttcta-atttgattcaaattgttgatgctctgcacctgcagTATCTTACCTTCAGGGCTGGCATGCCTTCAGAGAAATACATCCTTCTTTCTTGGTTCTCCACAGT

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: 49 (upstream exon), 41 (downstream exon)
Score: 39

ATTTTTCTTACAACCAGCTGTCAGGCAACTTTCCTTCTTGGACTACTCAGAACAATTTGCAACTGTGAGTATTGATTTCTGAAACTTCAAATGACCACCTgaaccatatc ... gcatctgcagTGTATTACCTTCAGGGCTGTCGTGTCTTCAGAGAGACACACCCTGTTTTCTTGGCTCTCCACAAT


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 89

ATTTTTCTTACAACCAGCTGTCAGGCAACTTTCCTTCTTGGACTACTCAGAACAATTTGCAACTGTGAGTATTGATTTCTGAAACTTCAAATGACCACCTgaaccatatc ... gcatctgcagTGTATTACCTTCAGGGCTGTCGTGTCTTCAGAGAGACACACCCTGTTTTCTTGGCTCTCCACAAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 115

ATTTTTCTTACAACCAGCTGTCAGGCAACTTTCCTTCTTGGACTACTCAGAACAATTTGCAACTGTGAGTATTGATTTCTGAAACTTCAAATGACCACCTgaaccatatc ... gcatctgcagTGTATTACCTTCAGGGCTGTCGTGTCTTCAGAGAGACACACCCTGTTTTCTTGGCTCTCCACAAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 98

ATTTTTCTTACAACCAGCTGTCAGGCAACTTTCCTTCTTGGACTACTCAGAACAATTTGCAACTGTGAGTATTGATTTCTGAAACTTCAAATGACCACCTgaaccatatc ... gcatctgcagTGTATTACCTTCAGGGCTGTCGTGTCTTCAGAGAGACACACCCTGTTTTCTTGGCTCTCCACAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttctcgcagcatatagattggattcataatgtcaatgttttgcatctgcagTGTATTACCTTCAGGGCTGTCGTGTCTTCAGAGAGACACACCCTGTTTTCTTGGCTCTCCACAAT
              atatagatt  TA-rich tract