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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATGgtaagtgcatgaatataagttccaaacgtcataaattagcaagtctacttacttgtaaaatgtttaggatgtatatgaataccatatggtattgatacta...

Basic information

species Zea mays
transcript GRMZM2G063492_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 9
ACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATGgtaagtgcatgaatataagttccaaacgtcataaattagcaagtctacttacttgtaaaatgtttaggatgtatatgaat-accatatggtattgatacta----
||| |||||||| ||||||||| ||||||||||||||||||| ||||||||||| ||| | || ||||| ||||| |  | |  |  |   ||| ||| |||| ||||| |||  | | |   ||| | ||| |||  | ||| ||| ||    |       | | ||    
ACACTCAACTGACAGAGAAGTTGCTATCATGATACTCATGGCGTACCTTTCATATATGCTGTCGATGgtgagtgcctacaaacta--taagaacttca-aaataagcaactctcttaagtc--aaattatttcggacatttatcaattacttcctccgtcccaaaatataag

upper sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA17G02560.1 (Glycine max), 5'ss of exon 7
ACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATGgtaagtgcatgaatataagttccaaacgtcataaattagcaagtctacttacttgtaaaatgtttag-gatgtatatgaataccatatggtattgatacta
 ||||| || ||  | || ||| || ||||| |||||||||||||||||||||| ||| ||||    |||||   ||      ||  || |  |  ||    || | | || ||   | ||  ||  || | |   || ||| |   |  ||                
GCATTCTACAGACCGTGAGGTTGCTCTCATGGTACTCATGGCATACCTTTCATATATGCTATCTGAAgtaagaaaattctctgaaactcgacccaccac--ctttgta-gtgtaaaaaattccaa--tgctaaccaatttatttctttggcag---------------
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|18963600|gb|BM660526.1|BM660526
EST:     AAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATG                         CTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATG
genomic: AAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATGgtaagtgcat ... caattttcagCTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATG
EST: gi|71311178|gb|DR791899.1|DR791899
EST:     AAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATG                         CTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATG
genomic: AAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATGgtaagtgcat ... caattttcagCTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATG
EST: gi|89106454|gb|DY576671.1|DY576671
EST:     AAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATG                         CTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATG
genomic: AAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATGgtaagtgcat ... caattttcagCTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATG
EST: gi|67026824|gb|CO455573.1|CO455573
EST:     AAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATG                         CTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATG
genomic: AAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATGgtaagtgcat ... caattttcagCTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATG

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: 47 (upstream exon), 47 (downstream exon)
Score: 164

ACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATGgtaagtgcat ... caattttcagCTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 292

ACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATGgtaagtgcat ... caattttcagCTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 306

ACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATGgtaagtgcat ... caattttcagCTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 218

ACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATGgtaagtgcat ... caattttcagCTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCA