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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACTATCAGAAGGAAACACCCTCATCTTTCAGTTTATCTCCACGTCTATCAATATTTCCACAATTTATGTTTAATTTAAGGCGTTCTCAGTTTGTTCAGgtaatctgtttctcatgttcattcagtcatgctgaacatatactctcagtttgatttagactattgagcggattgttgccacggatatctgcttgattat...

Basic information

species Oryza sativa
transcript LOC_Os08g36994.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g36994.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA03G22740.1 (Glycine max), 5'ss of exon 9
AGACTATCAGAAGGAAACACCCTCATCTTTCAGTTTATCTCCACGTCTATCAATATTTCCACAATTTATGTTTAATTTAAGGCGTTCTCAGTTTGTTCAGgtaatctgtttctcatgttcattcagtcatgctg-aacatatactctcagtttgatttag-actattgagcggattgttgccacggatatctgcttgattat--
 || | ||| || || || || || ||||||||||| |||||  |  | |||||||| || |||||||||||| ||||| | || ||||||||||||||||||     ||| |  ||||   |   | |   ||  | || |  || ||||   |||| | ||| |   |   | |  |    |  |  | |  || || |   
GGAATTTCAAAAAGACACTCCATCTTCTTTCAGTTTGTCTCCCAGGTTGTCAATATTCCCTCAATTTATGTTTCATTTACGACGCTCTCAGTTTGTTCAGgtatgtgttttatattgttggatttataagtttgtgatatttg-tcacagtaatattttgtactttaatgtttacttattttccttaattatattt-atcacag

upper sequence: LOC_Os08g36994.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA16G09260.1 (Glycine max), 5'ss of exon 3
AGACTATCAGAAGGAAACACCCTCATCTTTCAGTTTATCTCCACGTCTATCAATATTTCCACAATTTATGTTTAATTTAAGGCGTTCTCAGTTTGTTCAGgtaatctgtttctcatgttc--attcagtcatgctgaacatatactctcagtttgatttagactattgagcggattgttgccacggatatctgc-ttgattat--
 || | ||| || || || || || ||||||||||| |||||  |  | |||||||| || |||||||||||| ||||| | || ||||| |||||||||||| | ||||    ||  ||  |   |   | | |    ||||  |  ||||   |||| |    || |  |  |  ||        ||  |   || || |   
GGAATTTCAAAAAGACACTCCATCTTCTTTCAGTTTGTCTCCCAGGTTGTCAATATTCCCTCAATTTATGTTTCATTTACGACGCTCTCAATTTGTTCAGgta-tgtgttgtgtattgtcggagctatataagtttgtgatat-ttgccagtgatatttggtac-ttcaatgtttacttattttccttaattatatttatcacag

upper sequence: LOC_Os08g36994.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv15s0045g00540.t01 (Vitis vinifera), 5'ss of exon 11
AGACTATCAGAAGGAAACACCCTCATCTTTCAGTTTATCTCCACGTCTATCAATATTTCCACAATTTATGTTTAATTTAAGGCGTTCTCAGTTTGTTCAGgta-atctgtttctcatgttcattcagtcatgctg--aacatatactctcagtttgatttagactattgagcggattgttgccacggatatctgcttgatt-at------------------------
||| || || ||||| |  || || |||||||| ||||||||| |  | ||||||||||| || ||||| ||| ||||  | ||||||||||||||||||||| | |||  | |   ||| ||      ||  |   | | |||| ||  ||||||||   || || | |     | |   || |  || |   || |||| ||                        
AGATTACCAAAAGGACAACCCATCTTCTTTCAGCTTATCTCCAAGATTTTCAATATTTCCCCAGTTTATATTTCATTTGCGACGTTCTCAGTTTGTTCAGgtataactgactattg-gtttataattctatctttgcatcttataatcgtagtttgatgatgattaattact--ctcgccccctcttatcttctctagatttatctctggcaattctttttgtcacag

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|29622603|gb|CB627614.1|CB627614
EST:     CCACAATTTATGTTTAATNTAAGGCGTTCTCAGTTTGTTCAG                         GTGTTTAATAATAGTCCAGATGAAACTGCATATTTTAGGATGATGTTAAAC
genomic: CCACAATTTATGTTTAATTTAAGGCGTTCTCAGTTTGTTCAGgtaatctgtt ... tcccatgcagGTGTTTAATAATAGTCCAGATGAAACTGCATATTTTAGGATGATGTTAAAC
EST: gi|29622674|gb|CB627685.1|CB627685
EST:     CAATATTTCCACAATTTATGTTTAATTTAAGGCGTTCTCAGTTTGTTCAG                         GTGTTTAATAATAGTCCAGATGAAACTGCATATTTTAGGATGATGTTAAAC
genomic: CAATATTTCCACAATTTATGTTTAATTTAAGGCGTTCTCAGTTTGTTCAGgtaatctgtt ... tcccatgcagGTGTTTAATAATAGTCCAGATGAAACTGCATATTTTAGGATGATGTTAAAC
EST: gi|58656399|gb|CK045079.1|CK045079
EST:     CAATATTTCCACAATTTATGTTTAATTTAAGGCGTTCTCAGTTTGTTCAG                         GTGTCTAATAATAGTCCAGATGAAACTGCATATTTTAGGATGATGTTCAAC
genomic: CAATATTTCCACAATTTATGTTTAATTTAAGGCGTTCTCAGTTTGTTCAGgtaatctgtt ... tcccatgcagGTGTTTAATAATAGTCCAGATGAAACTGCATATTTTAGGATGATGTTAAAC

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: 69 (upstream exon), 72 (downstream exon)
Score: 23

AGACTATCAGAAGGAAACACCCTCATCTTTCAGTTTATCTCCACGTCTATCAATATTTCCACAATTTATGTTTAATTTAAGGCGTTCTCAGTTTGTTCAGgtaatctgtt ... tcccatgcagGTGTTTAATAATAGTCCAGATGAAACTGCATATTTTAGGATGATGTTAAACAGAGAGAATGTAGCGAATGCAGTTGTGATGATCCAGCCTTCACTTATAT




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