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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctactcagaccattttataaattgtgattatgtcactacctaagtgatgattatgttttaacactgttctatgtgatatggggaaaaacagGCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTGGCTCAACCGCGATCCTGATGCACCGACAGGGGGTGAGTTAATCTTTGGT

Basic information

species Oryza sativa
transcript LOC_Os01g18630.1
intron # 5
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|29645987|gb|CB650994.1|CB650994
EST:     CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTG                         GCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG
genomic: CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTGgtacctactc ... ggaaaaacagGCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG
EST: gi|300216028|gb|HO088654.1|HO088654
EST:     CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTG                         GCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTTTCCTTCTG
genomic: CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTGgtacctactc ... ggaaaaacagGCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG
EST: gi|117226899|gb|CT848683.1|CT848683
EST:     CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTG                         GCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTTTCCTTCTG
genomic: CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTGgtacctactc ... ggaaaaacagGCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG
EST: gi|29639114|gb|CB644123.1|CB644123
EST:     CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTG                         GCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG
genomic: CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTGgtacctactc ... ggaaaaacagGCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG
EST: gi|29643123|gb|CB648130.1|CB648130
EST:     CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTG                         GCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG
genomic: CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTGgtacctactc ... ggaaaaacagGCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG
EST: gi|29662753|gb|CB659028.1|CB659028
EST:     CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTG                         GCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG
genomic: CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTGgtacctactc ... ggaaaaacagGCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG
EST: gi|29665539|gb|CB661814.1|CB661814
EST:     CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTG                         GCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG
genomic: CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTGgtacctactc ... ggaaaaacagGCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG
EST: gi|29664681|gb|CB660956.1|CB660956
EST:     CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTG                         GCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG
genomic: CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTGgtacctactc ... ggaaaaacagGCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG
EST: gi|300215808|gb|HO088434.1|HO088434
EST:     CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTG                         GCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTTTCCTTCTG
genomic: CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTGgtacctactc ... ggaaaaacagGCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG
EST: gi|218504625|gb|FG968741.1|FG968741
EST:     CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTG                         GCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTTTCCTTCTG
genomic: CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTGgtacctactc ... ggaaaaacagGCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG
EST: gi|38471583|gb|CF955714.1|CF955714
EST:     CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTG                         GCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTTTCCTTCTG
genomic: CTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTGgtacctactc ... ggaaaaacagGCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTG

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: 65 (upstream exon), 75 (downstream exon)
Score: 79

CAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAGTTTGATGGAATTCTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAGCCCCTCCAATTTGgtacctactc ... ggaaaaacagGCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTGGCTCAACCGCGATCCTGATGCACCGACAGGGGGTGAGTTAATCTTTGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacctaagtgatgattatgttttaacactgttctatgtgatatggggaaaaacagGCAGGGAATGAAAGAGCAGCAACTGATCGAGAAGGATGTATTCTCCTTCTGGCTCAACCGCGATCCTGATGCACCGACAGGGGGTGAGTTAATCTTTGGT
                   ttttaac  putative branch site (score: 79)
          atgattatgttttaa  TA-rich tract