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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGGAGATGCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTGCTTTCTCAGgtttggcaagcaactccaatgatcgaattcttttgctagtgaccatatttgaagttgagtctaactcgtgcattgtcaattatgtttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g55500.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55500.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G437859_T01 (Zea mays), 5'ss of exon 5
----------------------------------------GTTGGGAGATGCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTGCTTTCTCAGgtttggcaagcaa----------ctcca-atgatcgaattcttttgctagtgaccatatttgaagttgagtctaactcgtgcattgtcaat-tatgtttttcag-----------
                                        |||||||||||||||||| |||| || |||||| | || || ||||||||||| |||||||| || |  ||||          ||||| || ||  | |||| |  |||   |||| |||     |   | | |  |   || |     || | ||  |||| |           
ATGGCTTGCTCATCCGATTGATGTCTGATAATTGCATCAGGTTGGGAGATGCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactggcaaaaaaaaaaaactccagattattcagttctct--ctacgcaccaaattcatgatcttggcgagtttaagcgtacctgatctctgcatttcggttgtttcgcag

upper sequence: LOC_Os01g55500.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G437859_T03 (Zea mays), 5'ss of exon 6
GTTGGGAGATGCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTGCTTTCTCAGgtttggcaagcaa----------ctcca-atgatcgaattcttttgctagtgaccatatttgaagttgagtctaactcgtgcattgtcaat-tatgtttttcag-----------
|||||||||||||||||| |||| || |||||| | || || ||||||||||| |||||||| || |  ||||          ||||| || ||  | |||| |  |||   |||| |||     |   | | |  |   || |     || | ||  |||| |           
GTTGGGAGATGCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactggcaaaaaaaaaaaactccagattattcagttctct--ctacgcaccaaattcatgatcttggcgagtttaagcgtacctgatctctgcatttcggttgtttcgcag
















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|58599082|gb|CK009610.1|CK009610
EST:     GCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTCGTCGTGCTTTCTCAG                         TATCTGAAGAATGTACAGATAAGAGATATTCCAATACTGGAGAGGTTCTCC
genomic: GCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTGCTTTCTCAGgtttggcaag ... tgtttttcagTATCTGAAGAATGTACAGATAAGAGATATTCCAATACTGGAGAGGTTCTCC
EST: gi|88358900|gb|CI619404.1|CI619404
EST:     GCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTGCTTTCTCAG                         TATCTGAAGAATGTACAGATAAGAGATATTCCAATACTGGAGAGGTTCTCC
genomic: GCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTGCTTTCTCAGgtttggcaag ... tgtttttcagTATCTGAAGAATGTACAGATAAGAGATATTCCAATACTGGAGAGGTTCTCC

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: 58 (upstream exon), 75 (downstream exon)
Score: 13

GTTGGGAGATGCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTGCTTTCTCAGgtttggcaag ... tgtttttcagTATCTGAAGAATGTACAGATAAGAGATATTCCAATACTGGAGAGGTTCTCCCTGTTCATCTGCATCGCGTTGGTTTGGGCCTATGCTCAAATCCTCACTG




<











<


<