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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACGgtatatcctctgatgataacaaaaataggaaatttggagtctatttgtattgtgttgcagcatgtgctgactccagaggcacttgaaaaaacataccatg...

Basic information

species Oryza sativa
transcript LOC_Os01g28680.3
intron # 4
splice site 5'
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|33674946|gb|CF303185.1|CF303185
EST:     ATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACG                         CAAGTTCACGAAAGGCTTGGAGTTTTCGAATGATGATGATGGGTTCTCCTT
genomic: ATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACGgtatatcctc ... tataatgcagCAAGTTCACGAA-GGCTTGGAGTTTTCGAATGATGATGATGGGTTCTCCTT
EST: gi|33795075|gb|CF323413.1|CF323413
EST:     ATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACG                         CAAGTTCACGAAGGCTTTGGAGTTTTCGAATGATGA
genomic: ATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACGgtatatcctc ... tataatgcagCAAGTTCACGAAGGCTT-GGAGTTTTCGAATGATGA
EST: gi|29612829|gb|CB617842.1|CB617842
EST:     ATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACG                         CAAGTTCACGAAGGCTTGGAGTTCTCTAATGATGATGATGGGTTCTCCTTT
genomic: ATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACGgtatatcctc ... tataatgcagCAAGTTCACGAAGGCTTGGAGTTTTCGAATGATGATGATGGGTTCTCCTTT
EST: gi|29688485|gb|CB684760.1|CB684760
EST:     ATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACG                         CAAGTTCACGAAGGCTTGGAGTTTTCGAATGATGATGATGGGTTCTCCTTT
genomic: ATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACGgtatatcctc ... tataatgcagCAAGTTCACGAAGGCTTGGAGTTTTCGAATGATGATGATGGGTTCTCCTTT
EST: gi|33676806|gb|CF305045.1|CF305045
EST:     ATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACG                         CAAGTTCACGAAAGCTTGGAGTTTTCCAATGATGATGATGGGT
genomic: ATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACGgtatatcctc ... tataatgcagCAAGTTCACGAAGGCTTGGAGTTTTCGAATGATGATGATGGGT
EST: gi|33693127|gb|CF321366.1|CF321366
EST:     ATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACG                         CAAGTTCACGAAGGCTTGGAGTTTTCGAATGATGATGATGGGTTCTCCTTT
genomic: ATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACGgtatatcctc ... tataatgcagCAAGTTCACGAAGGCTTGGAGTTTTCGAATGATGATGATGGGTTCTCCTTT

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), 75 (downstream exon)
Score: 56

GCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACGgtatatcctc ... tataatgcagCAAGTTCACGAAGGCTTGGAGTTTTCGAATGATGATGATGGGTTCTCCTTTGCCATATTTTCTGTTAAGTTTTCAAAAGATGGCCGAGAACTTGTTGTTG




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