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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGAAGATGCTGTTGTGGTTGCACTTGGTCAACACCGGAGACCTAGTATAGTTCGGCAATTCACATCAGgtttgcacttcttttatcatttcatatcattcttgtttaacttacatgcgtaatatgatttcttcattggtgctgccttcactcataaaaaaaaactaagaaaggtataaattcttctcttatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g70320.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70320.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G126266_T01 (Zea mays), 5'ss of exon 12
GTGGAAGATGCTGTTGTGGTTGCACTTGGTCAACACCGGAGACCTAGTATAGTTCGGCAATTCACATCAGgtttgcacttcttttatcatttcatatcattcttgtttaacttacatgcgtaatatgatttcttcattggtgctgccttcactcataaaaaaaaactaagaaaggta-taaattcttctcttatgcag
||||||||||||||||| |||||| |||| ||||| || |||||||| |||||||| || |||||||||||||||   |  |||| | || |  | || |  |  ||  | | | ||      ||| |||  ||| ||     |||| |         ||  ||| ||  || |||| |||||| |    ||      
GTGGAAGATGCTGTTGTAGTTGCAGTTGGCCAACATCGCAGACCTAGCATAGTTCGTCAGTTCACATCAGgtttgg--tgtttttgttatattttctc-tcttcattccaatgaaat------tataattgattcttt-----tgccat---------aagtaaagtattaatggtactaaattttatggttg-----
















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|29626303|gb|CB631314.1|CB631314
EST:     TGCACTTGGTCAACACCGGAGACNTAGTATAGTTCGGCAATTCACATCAG                         ATTTTAAATCACCTGGTGAACCTAAATTCTTGGAGGCGTTTG
genomic: TGCACTTGGTCAACACCGGAGACCTAGTATAGTTCGGCAATTCACATCAGgtttgcactt ... tcttatgcagATTTTAAATCACCTGGTGAACCTAAATTCTTGGAGGCGTTTG
EST: gi|29667592|gb|CB663867.1|CB663867
EST:     TGCACTTGGTCAACACCGGAGACCTAGTATAGTTCGGCAATTCACATCAG                         ATTTTAAATCACCTGGTGAACCTAAATTCTTGGAGGCGTTTG
genomic: TGCACTTGGTCAACACCGGAGACCTAGTATAGTTCGGCAATTCACATCAGgtttgcactt ... tcttatgcagATTTTAAATCACCTGGTGAACCTAAATTCTTGGAGGCGTTTG
EST: gi|58595919|gb|CK006447.1|CK006447
EST:     TGCACTTGGTCAACACCGGAGACCTAGTATAGTTCGGCAATTCACATCAG                         ATTTTAAATCACCTGGTGAACCTAAATTCTTGGAGGCGTTTG
genomic: TGCACTTGGTCAACACCGGAGACCTAGTATAGTTCGGCAATTCACATCAGgtttgcactt ... tcttatgcagATTTTAAATCACCTGGTGAACCTAAATTCTTGGAGGCGTTTG
EST: gi|218479946|gb|FG955453.1|FG955453
EST:     TGCACTTGGTCAACACCGGAGACCTAGTATAGTTCGGCAATTCACATCAG                         ATTTTAAATCACCTGGTGAACCTAAATTCTTGGAGGCGTTTG
genomic: TGCACTTGGTCAACACCGGAGACCTAGTATAGTTCGGCAATTCACATCAGgtttgcactt ... tcttatgcagATTTTAAATCACCTGGTGAACCTAAATTCTTGGAGGCGTTTG

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: 63 (upstream exon), 42 (downstream exon)
Score: 14

GTGGAAGATGCTGTTGTGGTTGCACTTGGTCAACACCGGAGACCTAGTATAGTTCGGCAATTCACATCAGgtttgcactt ... tcttatgcagATTTTAAATCACCTGGTGAACCTAAATTCTTGGAGGCGTTTG




<











<


<