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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttgggatttatactgcctccaaaattgcattagttgttgaatggattttccatgtactgacctggtgctattttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAG

Basic information

species Oryza sativa
transcript LOC_Os02g10070.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 11
gtatgcttgggatttatactgcctccaaaattgcattagttgttgaatggat--tttccatgtactgacctggtgctattttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAG
|||  |||||||||| ||||| | |     |    |||  |||| | ||| |  ||||||||   |   |   |  | |||  ||||||| ||||||||||| |||||||| ||||||||  |||| ||||| |||||| |||||||||| ||||||||||||||
gtaaacttgggatttgtactgtcac-----tcattttatgtgttcagtggttgctttccatggtgttcacaattattgtttgtatagGTTTTGGGAGCCTACTTATGAAGACTGCTTAAACATGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G063851_T01 (Zea mays), 3'ss of exon 11
gtatgcttgggatttatactgcctccaaaattgcattagttgttgaatggattttccatgtactgacctgg--tgctattttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAG
|||  |||||||||| |||||||||| |  ||   |||  |||| | ||| |  |   | |  ||  |     |  | |||  ||||||| ||||||||||| |||||||| |||||||||||||| ||||| |||||| |||||||||| ||||||||||||||
gtaaacttgggatttgtactgcctccca--ttttcttatgtgttcagtggttgctttctatggtggtcaaaattattgtttgtatagGTTTTGGGAGCCTACTTATGAAGACTGCTTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G063909_T02 (Zea mays), 3'ss of exon 9
gtatgcttgggatttatactgcctccaaaattgcattagttgttgaatggattttccatgtactgacctggtgctattttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAG
|||  |||||||||    |    | |  || ||  | ||| ||||       ||| ||||   |   |   |  | |||  ||||| | ||||||||||| |||||||| |||||||||||||| ||||| |||||| |||||||||| ||||||||||||||
gtaaacttgggattccacccattttcttaagtgt-tcagtggttg------cttttcatggtgttcacaattattgtttgtatagGCTTTGGGAGCCTACTTATGAAGACTGCTTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG

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|58695418|gb|CK084105.1|CK084105
EST:     GTGGAGAGTGAGTTTCAAAAAGCCTATGACAAAGGAATGTCAAAATCAAA                         GTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCC
genomic: GTGGAGAGTGAGTTTCAAAAAGCCTATGACAAAGGAATGTCAAAATCAAAgtatgcttgg ... attttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCC
EST: gi|29614058|gb|CB619071.1|CB619071
EST:     GTGGAGAGTGAGTTTCAAAAAGCCTATGACAAAGGAATGTCAAAATCAAA                         GTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCC
genomic: GTGGAGAGTGAGTTTCAAAAAGCCTATGACAAAGGAATGTCAAAATCAAAgtatgcttgg ... attttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCC
EST: gi|14571277|gb|BI118645.1|BI118645
EST:     GTGGAGAGTGAGTTTCAAAAAGCCTATGACAAAGGAATGTCAAAATCAAA                         GTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCC
genomic: GTGGAGAGTGAGTTTCAAAAAGCCTATGACAAAGGAATGTCAAAATCAAAgtatgcttgg ... attttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCC
EST: gi|58599089|gb|CK009617.1|CK009617
EST:     GTGGAGAGTGAGTTTCAAAAAGCCTATGACAAAGGAATGTCAAAATCAAA                         GTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCC
genomic: GTGGAGAGTGAGTTTCAAAAAGCCTATGACAAAGGAATGTCAAAATCAAAgtatgcttgg ... attttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCC
EST: gi|29614020|gb|CB619033.1|CB619033
EST:     GTGGAGAGTGAGTTTCAAAAAGCCTATGACAAAGGAATGTCAAAATCAAA                         GTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGAT
genomic: GTGGAGAGTGAGTTTCAAAAAGCCTATGACAAAGGAATGTCAAAATCAAAgtatgcttgg ... attttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGAT
EST: gi|33794508|gb|CF323141.1|CF323141
EST:     GTGGAGAGTGAGTTTCAAAAAGCCTATGACAAAGGAATGTCAAAATCAAA                         GTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCC
genomic: GTGGAGAGTGAGTTTCAAAAAGCCTATGACAAAGGAATGTCAAAATCAAAgtatgcttgg ... attttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCC
EST: gi|58668188|gb|CK056874.1|CK056874
EST:     GTGGAGAGTGAGTTTCAAAAAGCCTATGACAAAGGAATGTCAAAATCAAA                         GTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCC
genomic: GTGGAGAGTGAGTTTCAAAAAGCCTATGACAAAGGAATGTCAAAATCAAAgtatgcttgg ... attttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCC

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: 66 (upstream exon), 50 (downstream exon)
Score: 53

GTGGAGAGTGAGTTTCAAAAAGCCTATGACAAAGGAATGTCAAAATCAAAgtatgcttgg ... attttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcattagttgttgaatggattttccatgtactgacctggtgctattttaatagGTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAG
                              tactgac  putative branch site (score: 53)
                                           ctatttt  putative PPT
                                            tattttaata  TA-rich tract