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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatgcatgcatagtctctatgcacaataccacgaatgcctcctaattcttggctgtttcctcactcagGTATATGCAAGTACATCCCGTGATAGTTTACTTGCAACAGTTCTTGATGTTTTACAAAACCAG

Basic information

species Oryza sativa
transcript LOC_Os10g42439.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G367023_T01 (Zea mays), 3'ss of exon 5
gtaagtatgcatgcata---gtctctatgcacaataccacgaatgcctcctaattcttggctgtttcctcactcagGTATATGCAAGTACATCCCGTGATAGTTTACTTGCAACAGTTCTTGATGTTTTACAAAACCAG
|||||||  || |||||   |||||||| || | |||    |||| |  |||||| ||  || | |  |  |||||||||||||||| || |||||||||| | |||||||||||||||||||  ||||||||| ||||
gtaagtagaca-gcatacaggtctctatcca-attacaggaaatgtcatctaattgtt--ctatgttttttctcagGTATATGCAAGCACTTCCCGTGATAATCTACTTGCAACAGTTCTTGACATTTTACAAACCCAG

upper sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G049288_T01 (Zea mays), 3'ss of exon 5
gtaagtatgcat-gcatag-tctctatgcacaataccacgaatgcctcctaattcttggctgtttcctcactcagGTATATGCAAGTACATCCCGTGATAGTTTACTTGCAACAGTTCTTGATGTTTTACAAAACCAG
|||||||   ||   | || ||||||| | || |||    |||||    ||||| ||   |||||     |||||||||||||||| || |||||||||| | |||||||||||||||||||||||||| ||| ||||
gtaagtacatatcatacaggtctctatcc-cattacaggaaatgctatgtaattattctgtgttttt---ctcagGTATATGCAAGCACTTCCCGTGATAATCTACTTGCAACAGTTCTTGATGTTTTAGAAACCCAG
















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: 70 (upstream exon), 75 (downstream exon)
Score: 15

TATCATTGTTCGACCTCTCTCAACAGTAAGTGCCCTTGTGCGATTTGCAGAAGAACCGCAGATGTTTGCATTCGAATTCAATGATGGTTGCCCGATTCATgtaagtatgc ... cctcactcagGTATATGCAAGTACATCCCGTGATAGTTTACTTGCAACAGTTCTTGATGTTTTACAAAACCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctatgcacaataccacgaatgcctcctaattcttggctgtttcctcactcagGTATATGCAAGTACATCCCGTGATAGTTTACTTGCAACAGTTCTTGATGTTTTACAAAACCAG
                                            tcctcac  putative branch site (score: 15)
                                       ctgtttcctcactc  CT-rich tract
                             taattctt  TA-rich tract