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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAGATGAGTTCTCAATCTTTTCGCCCTCCAAAACCTGAAGATATTGCCACTATTTGTTACACTAGTGGCACTACTGGCACACCGAAGgtaaataactcatctttctgattatttttagtttcattcaaagagctcttctaattcaaccttccaatctgtgacgatgtcatatttatttcag

Basic information

species Oryza sativa
transcript LOC_Os12g04990.4
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04990.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 1
----------GGAAAGATGAGTTCTCAATCTTTTCGCCCTCCAAAACCTGAAGATATTGCCACTATTTGTTACACTAGTGGCACTACTGGCACACCGAAGgtaaataactcatctttctgattatttttagtttcattcaaagagctcttctaattcaaccttcca-atctgtgac----gatgtcatatttatttcag
          ||||||   ||| ||||| ||||| | | |||||||||||||||| |||||||||| |||||||||||||||||||||||||||||||||||||||    |||| ||||||||||| || | |||||    | || |||| || ||  || || |  ||| ||||     ||| |||| ||| | ||||
CTTCACTCAGGGAAAGGGAAGTCCTCAACCTTTTTGTCTTCCAAAACCTGAAGATGTTGCCACTATCTGTTACACTAGTGGCACTACTGGCACACCGAAGgtaaatcggccatccttctgattattctttgcttcatcagcaaagttcttttacttgtacatttcggatcggtgatattggatatcat-tttttctcag
















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|58655107|gb|CK043787.1|CK043787
EST:     AAGATATTGCCACTATTTGTTACACTAGTGGCACTACTGGCACACCGAAG                         GGAGTTGTTCTTTCTCATGGGAATTTAATTGCAAATGTAGCAGGATCAAGC
genomic: AAGATATTGCCACTATTTGTTACACTAGTGGCACTACTGGCACACCGAAGgtaaataact ... tttatttcagGGAGTTGTTCTTTCTCATGGGAATTTAATTGCAAATGTAGCAGGATCAAGC
EST: gi|58694148|gb|CK082835.1|CK082835
EST:     AAGATATTGCCACTATTTGTTACACTAGTGGCACTACTGGCACACCGAAG                         GGAGTTGTTCTTTCTCATGGGAATTTAATTGCAAATGTAGCAGGATCAAGC
genomic: AAGATATTGCCACTATTTGTTACACTAGTGGCACTACTGGCACACCGAAGgtaaataact ... tttatttcagGGAGTTGTTCTTTCTCATGGGAATTTAATTGCAAATGTAGCAGGATCAAGC
EST: gi|58689916|gb|CK078603.1|CK078603
EST:     AAGATATTGCCACTATTTGTTACACTAGTGGCACTACTGGCACACCGAAG                         GGAGTTGTTCTTTCTCATGGGAATTTAATTGCAAATGTAGCAGGATCAAGC
genomic: AAGATATTGCCACTATTTGTTACACTAGTGGCACTACTGGCACACCGAAGgtaaataact ... tttatttcagGGAGTTGTTCTTTCTCATGGGAATTTAATTGCAAATGTAGCAGGATCAAGC
EST: gi|58666789|gb|CK055475.1|CK055475
EST:     AAGATATTGCCACTATTTGTTACACTAGTGGCACTACTGGCACACCGAAG                         GGAGTTGTTCTTTCTCATGGGAATTTAATTGCAAATGTAGCAGGATCAAGC
genomic: AAGATATTGCCACTATTTGTTACACTAGTGGCACTACTGGCACACCGAAGgtaaataact ... tttatttcagGGAGTTGTTCTTTCTCATGGGAATTTAATTGCAAATGTAGCAGGATCAAGC

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: 50 (upstream exon), 65 (downstream exon)
Score: 15

GGAAAGATGAGTTCTCAATCTTTTCGCCCTCCAAAACCTGAAGATATTGCCACTATTTGTTACACTAGTGGCACTACTGGCACACCGAAGgtaaataact ... tttatttcagGGAGTTGTTCTTTCTCATGGGAATTTAATTGCAAATGTAGCAGGATCAAGCCTAGTCATTAAGTTTTACCCATCTGATGT




<











<


<