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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtcttcttcactctccagctatgttctgcaaaataatcaagcttttgtttgtggaataagtgctcaaaattcttgcagAAGATTCAAATCGAGATTCAAAGAAGTTGAAGCCTGTCGACAGCGAACCCATTTCTCCTGCTGAAACTGATGTTAACCAGCTTCCAATTATCTTGTCTGA

Basic information

species Oryza sativa
transcript LOC_Os08g39310.1
intron # 3
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|29643027|gb|CB648034.1|CB648034
EST:     CAAGATGAACAAGCTTTTAGCTAAGCATATTAGACCACTTGAGGCNNNNN                         NNGATTCAAATCGAGATTCAAAGAAGTTGAAGCCTGTCGACAGCGAACCCA
genomic: CAAGATGAACAAGCTTTTAGCTAAGCATATTAGACCACTTGAGGCAAAAAgtaggtcttc ... attcttgcagAAGATTCAAATCGAGATTCAAAGAAGTTGAAGCCTGTCGACAGCGAACCCA
EST: gi|29619019|gb|CB624031.1|CB624031
EST:     AAGATGAACAAGC-TTTAGCTAAAGCATATTAGACCACTTGAGGCNNNNN                         NNGATTCAAATCGAGATTCAAAGAAGTTGAAGCCTGTCGACAGCGAACCCA
genomic: AAGATGAACAAGCTTTTAGCT-AAGCATATTAGACCACTTGAGGCAAAAAgtaggtcttc ... attcttgcagAAGATTCAAATCGAGATTCAAAGAAGTTGAAGCCTGTCGACAGCGAACCCA
EST: gi|29682543|gb|CB678818.1|CB678818
EST:     CAAGATGAACAAGCTTTTACCTAAGCATATTATACCACTTGAGGCNNNNN                         NNGATTCAAATCGAGATTCAAAGAAGTTGAAGCCTGTCGACAGCGAACCCA
genomic: CAAGATGAACAAGCTTTTAGCTAAGCATATTAGACCACTTGAGGCAAAAAgtaggtcttc ... attcttgcagAAGATTCAAATCGAGATTCAAAGAAGTTGAAGCCTGTCGACAGCGAACCCA
EST: gi|29619017|gb|CB624029.1|CB624029
EST:     CAAGATGAACAAGCTTTTAGCTAAGCATATTAGACCACTTGAGGCNNNNN                         NNGATTCAAATCGAGATTCAAAGAAGTTGAAGCCTGTCGACAGCGAACCCA
genomic: CAAGATGAACAAGCTTTTAGCTAAGCATATTAGACCACTTGAGGCAAAAAgtaggtcttc ... attcttgcagAAGATTCAAATCGAGATTCAAAGAAGTTGAAGCCTGTCGACAGCGAACCCA

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: 63 (upstream exon), 50 (downstream exon)
Score: 20

TGCAATGATGAGCTGCGTCTAGTCTTTGAGACAGATAGCACTGATATGTTCAAGATGAACAAGCTTTTAGCTAAGCATATTAGACCACTTGAGGCAAAAAgtaggtcttc ... attcttgcagAAGATTCAAATCGAGATTCAAAGAAGTTGAAGCCTGTCGACAGCGAACCCATTTCTCCTGCTGAAACTGATGTTAACCAGCTTCCAATTATCTTGTCTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgcaaaataatcaagcttttgtttgtggaataagtgctcaaaattcttgcagAAGATTCAAATCGAGATTCAAAGAAGTTGAAGCCTGTCGACAGCGAACCCATTTCTCCTGCTGAAACTGATGTTAACCAGCTTCCAATTATCTTGTCTGA
                                              ttcttgc  CT-rich tract
      aaaataatcaa  TA-rich tract