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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtatatatgccgtagactctcgatctgcttggagtttacaaacgtgacagatgtgatttctcaatgttggtattctattttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG

Basic information

species Oryza sativa
transcript LOC_Os11g39650.1
intron # 8
splice site 3'
intron type U2

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|86506017|gb|CI148650.1|CI148650
EST:     AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|86498028|gb|CI140661.1|CI140661
EST:     AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|29675265|gb|CB671540.1|CB671540
EST:     AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|29665512|gb|CB661787.1|CB661787
EST:     AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|87011566|gb|CI279475.1|CI279475
EST:     AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|86495429|gb|CI138062.1|CI138062
EST:     AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|29671178|gb|CB667453.1|CB667453
EST:     AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|87028003|gb|CI276359.1|CI276359
EST:     ATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: ATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|86498891|gb|CI141524.1|CI141524
EST:     GGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: GGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|218487277|gb|FG955018.1|FG955018
EST:     AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|218488104|gb|FG955050.1|FG955050
EST:     AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|86498140|gb|CI140773.1|CI140773
EST:     AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|86495472|gb|CI138105.1|CI138105
EST:     AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|86493402|gb|CI136035.1|CI136035
EST:     AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|87011559|gb|CI279468.1|CI279468
EST:     AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|86492827|gb|CI135460.1|CI135460
EST:     ATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: ATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|86498441|gb|CI141074.1|CI141074
EST:     AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|86494509|gb|CI137142.1|CI137142
EST:     AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: AAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
EST: gi|88222357|gb|CI222313.1|CI222313
EST:     TGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAG                         GACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG
genomic: TGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGG

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: 72 (upstream exon), 71 (downstream exon)
Score: 13

GCATTATTGTACTAAGTTCAAAAAATATGCGGTCGCTTGTAACAGTTAAAAAGGCACATCTTGGCATTATTACTACATTGGCATTCTCTCAAGATTCAAGgtcagtatat ... tttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttacaaacgtgacagatgtgatttctcaatgttggtattctattttatatcagGACCTTGCTGTCGACTTCCTTCGATTCTACTGCTAGGGTGACTTCAATTGGATCACCTAAGAGTCGTG
                                       ttctatttt  CT-rich tract
                                     tattctattttatatc  TA-rich tract