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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggtgctttatacattttgatattattgatgcaagtggtggtatatttgaaaaaaaaacacataaatatgtgtgttctgttactttacagTTTGATATCCTGTGGGATGCATTAACAGCTAAAGAGCACATGGAATTGTTTGCCAGCATCAAGGGATTGCATCCAGCAGCAATCACATCA

Basic information

species Zea mays
transcript GRMZM2G142249_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142249_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g30740.1 (Oryza sativa), 3'ss of exon 10
gt-ggtgctttatacattttgatattattgatgcaagtggtggtatatttgaaaaaaaaacacataaatatgtgtgttctgttactttacagTTTGATATCCTGTGGGATGCATTAACAGCTAAAGAGCACATGGAATTGTTTGCCAGCATCAAGGGATTGCATCCAGCAGCAATCACATCA
|| ||||||||| ||||| | |||||| ||||||| |||       | ||||  |||  | | ||||| ||  ||| | | || |||| |||||||| ||| ||||||||||  ||||||||||||||||||||||  ||||||| ||||| |||||| ||| |||| || ||||||  || 
gtaggtgctttaaacattgttatattactgatgcatgtg-------aattgatcaaagga-agataaacattcgtgatttatttctttgcagTTTGACATCTTGTGGGATGCGCTAACAGCTAAAGAGCACATGGAGCTGTTTGCTAGCATTAAGGGACTGCCTCCATCAACAATCAAGTCG
















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: 43 (upstream exon), 49 (downstream exon)
Score: 16

CATTCATTTATGGTCACTCTGTTCGAAGCACTGTGGGAATGTCAAACATCCGTAGGATGATCGGAGTCTGCCCACAGgtggtgcttt ... tactttacagTTTGATATCCTGTGGGATGCATTAACAGCTAAAGAGCACATGGAATTGTTTGCCAGCATCAAGGGATTGCATCCAGCAGCAATCACATCA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 304

CATTCATTTATGGTCACTCTGTTCGAAGCACTGTGGGAATGTCAAACATCCGTAGGATGATCGGAGTCTGCCCACAGgtggtgcttt ... tactttacagTTTGATATCCTGTGGGATGCATTAACAGCTAAAGAGCACATGGAATTGTTTGCCAGCATCAAGGGATTGCATCCAGCAGCAATCACATCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 447

CATTCATTTATGGTCACTCTGTTCGAAGCACTGTGGGAATGTCAAACATCCGTAGGATGATCGGAGTCTGCCCACAGgtggtgcttt ... tactttacagTTTGATATCCTGTGGGATGCATTAACAGCTAAAGAGCACATGGAATTGTTTGCCAGCATCAAGGGATTGCATCCAGCAGCAATCACATCA


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 68

CATTCATTTATGGTCACTCTGTTCGAAGCACTGTGGGAATGTCAAACATCCGTAGGATGATCGGAGTCTGCCCACAGgtggtgcttt ... tactttacagTTTGATATCCTGTGGGATGCATTAACAGCTAAAGAGCACATGGAATTGTTTGCCAGCATCAAGGGATTGCATCCAGCAGCAATCACATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtggtatatttgaaaaaaaaacacataaatatgtgtgttctgttactttacagTTTGATATCCTGTGGGATGCATTAACAGCTAAAGAGCACATGGAATTGTTTGCCAGCATCAAGGGATTGCATCCAGCAGCAATCACATCA
                                       ttctgtt  CT-rich tract
      tatatttgaaaaaaaa  TA-rich tract