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'   		22  
 5'  3'   		23  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgtcttactcttattgtcatgcttcaacaatttgggattattagtttctcaaaaacctttttatttgcagGTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATGATGGTTCTTGATACACATGGGGAAGTCTTTGTTTGGATGGGTCAGTGTG

Basic information

species Oryza sativa
transcript LOC_Os03g24220.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G359566_T01 (Zea mays), 3'ss of exon 2
---------------gtatgttgtcttactcttatt--gtcatgcttcaacaatttgggattattagtt-------tctcaaaaacctttttatttgcagGTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATGATGGTTCTTGATACACATGGGGAAGTCTTTGTTTGGATGGGTCAGTGTG
                | | |||  ||  ||  | |  ||  || | ||  ||| | |  || ||||         |    ||| |    || |  |||||| |||||||||||||| |||||||||||||||||| |||| |||||||||||| | |||||||||||    || || ||||| |||||||||||||| |
gctggaggtttgttgctctattgatttgatccaaattggttgtgttccagtaatcttgtttttttagaaaaaaaaatactgaaagctcacttgtacgcagGTTACTGAAATTTTCAATTTTTCACAAGATGATTTGTTGACCGAAGACATGATGATACTTGATACACACTCTGAGGTTTTTGTCTGGATGGGTCAGTGCG

upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 18
--------gtatgttgtcttactcttatt--gtcatgcttcaacaatttgggattatt---agtttctcaaaaacctttttatttgcagGTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATGATGGTTCTTGATACACATGGGGAAGTCTTTGTTTGGATGGGTCAGTGTG----------------------------
         | | |||  ||  ||  | |  ||| || | ||  ||| | |  || ||   | |      ||| |    || |  |||||| |||||||||||||| ||||||||||||||| || |||| |||||||||||| | |||||||||||  | || || ||||||||||||||||||||||                            
gtttgtttctgtattgatttgatccaaattggtcttgttccagtaatcttgctttttttaaaataatctgaaagctcacttgtacgcaggttactgaaattttcaatttttcacaagATGATCTGTTGACCGAAGACATGATGATACTTGATACACACTGTGAGGTTTTTGTTTGGATGGGTCAGTGTGTGGAGACAAAAGAAAAACAGAAAGCATT
















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|88694289|gb|CI738327.1|CI738327
EST:     TGAGGAATGGGAAACTGGAG                         GTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG
genomic: TGAGGAATGGGAAACTGGAGgtatgttgtc ... ttatttgcagGTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG
EST: gi|58596217|gb|CK006745.1|CK006745
EST:     CTCATTGAGGAATGGGAAACTGGAG                         GTCACTGAAATTTTCAACTTTTCACAAGATGATTGGGTGACTGAAGACATG
genomic: CTCATTGAGGAATGGGAAACTGGAGgtatgttgtc ... ttatttgcagGTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG
EST: gi|88351837|gb|CI624642.1|CI624642
EST:     CTCATTGAGGAATGGGAAACTGGAG                         GTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG
genomic: CTCATTGAGGAATGGGAAACTGGAGgtatgttgtc ... ttatttgcagGTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG
EST: gi|25798468|gb|CA754429.1|CA754429
EST:     CTCATTGAGGAATGGGAAACTGGAG                         GTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG
genomic: CTCATTGAGGAATGGGAAACTGGAGgtatgttgtc ... ttatttgcagGTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG
EST: gi|396941448|gb|HO188657.1|HO188657
EST:     CTCATTGAGGAATGGGAAACTGGAG                         GTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG
genomic: CTCATTGAGGAATGGGAAACTGGAGgtatgttgtc ... ttatttgcagGTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG
EST: gi|88722817|gb|CI746327.1|CI746327
EST:     CTCATTGAGGAATGGGAAACTGGAG                         GTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTG
genomic: CTCATTGAGGAATGGGAAACTGGAGgtatgttgtc ... ttatttgcagGTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTG
EST: gi|33674859|gb|CF303098.1|CF303098
EST:     CTCATTGAGGAATGGGAAACTGGAG                         GTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG
genomic: CTCATTGAGGAATGGGAAACTGGAGgtatgttgtc ... ttatttgcagGTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG
EST: gi|58674368|gb|CK063054.1|CK063054
EST:     CTCATTGAGGAATGGGAAACTGGAG                         GTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG
genomic: CTCATTGAGGAATGGGAAACTGGAGgtatgttgtc ... ttatttgcagGTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG
EST: gi|58610643|gb|CK038355.1|CK038355
EST:     CTCATTGAGGAATGGGAAACTGGAG                         GTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG
genomic: CTCATTGAGGAATGGGAAACTGGAGgtatgttgtc ... ttatttgcagGTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG
EST: gi|58672994|gb|CK061680.1|CK061680
EST:     CTCATTGAGGAATGGGAAACTGGAG                         GTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG
genomic: CTCATTGAGGAATGGGAAACTGGAGgtatgttgtc ... ttatttgcagGTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATG

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: 11 (upstream exon), 75 (downstream exon)
Score: 46

GGAAACTGGAGgtatgttgtc ... ttatttgcagGTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATGATGGTTCTTGATACACATGGGGAAGTCTTTGTTTGGATGGGTCAGTGTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcatgcttcaacaatttgggattattagtttctcaaaaacctttttatttgcagGTCACTGAAATTTTCAACTTTTCACAAGATGATTTGCTGACTGAAGACATGATGGTTCTTGATACACATGGGGAAGTCTTTGTTTGGATGGGTCAGTGTG
                                        cctttttattt  CT-rich tract
                                   aaaaacctttttattt  TA-rich tract