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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCATCAGCTCTTCTTAGTGCTGCATTTGTGTATGATGTTTTCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcatgatttttatttttttgcaacaatctttttattacttactgtttagtactgtggatttatccagtggtgataatagtaccataatatgctg...

Basic information

species Oryza sativa
transcript LOC_Os11g24540.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g24540.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G082330_T01 (Zea mays), 5'ss of exon 10
GTTGCATCAGCTCTTCTTAGTGCTGCATTTGTGTATGATGTTTTCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcatgatttttatttttttgcaacaatctttttattacttactgtttagtactgtggatt--tatccagtggtgataatagtaccataatat-gctg-
|||||||| || ||||||||||||||||||||||||||  | || ||||||||||||||||||||||||||||||||||| ||||||||||||||||||| || | || |    |   |  |   |  | | | |  | | | ||||||||    | ||  |||  |     || |    |   |    ||  ||  
GTTGCATCGGCACTTCTTAGTGCTGCATTTGTGTATGACATCTTTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCAgtaagtgtatcaattct----tacagtgaagcttatgtaaatggtaattttttagtacgacaggttgatatgtaacatagacatagttgttaaggcatcactta
















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|2310019|gb|C26174.1|C26174
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|38474789|gb|CF958922.1|CF958922
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|58691853|gb|CK080540.1|CK080540
EST:     TGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCCATTCCGATGCTCTTAAGAATA
genomic: TGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|286796|gb|D15603.1|D15603
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGAA                         GTTGCTCGTGGTGATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATA
EST: gi|58591329|gb|CF989637.1|CF989637
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|29664759|gb|CB661034.1|CB661034
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|25799734|gb|CA755695.1|CA755695
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|29667214|gb|CB663489.1|CB663489
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|29641729|gb|CB646736.1|CB646736
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|218478582|gb|FG949084.1|FG949084
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|396941284|gb|HO188493.1|HO188493
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|27578188|gb|CB000883.1|CB000883
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|29633639|gb|CB638648.1|CB638648
EST:     ATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: ATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|29677381|gb|CB673656.1|CB673656
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|86426221|gb|CI071318.1|CI071318
EST:     TATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|218501626|gb|FG955998.1|FG955998
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|218504564|gb|FG954781.1|FG954781
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA

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: 75 (upstream exon), 70 (downstream exon)
Score: 57

GTTGCATCAGCTCTTCTTAGTGCTGCATTTGTGTATGATGTTTTCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG




<











<


<