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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacaagctgattaattaccaatttagctgacagcaacttgaggtgtgcttctgttaaatggattaacgaagaatctcatcgttttttttccctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAGGCTTTCAGTGTTCTCTGTTTCTTCGCACCTGTCTGTAATTATTCGTGTA

Basic information

species Oryza sativa
transcript LOC_Os01g41220.2
intron # 1
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|88210746|gb|CI210595.1|CI210595
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTAC------AAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88204837|gb|CI202688.1|CI202688
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGT----                         --CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88998026|gb|CI037911.1|CI037911
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTAC------AAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86823314|gb|CI256319.1|CI256319
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGT----                         --CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86420048|gb|CI054849.1|CI054849
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88236964|gb|CI236813.1|CI236813
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGT----                         --CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|87028437|gb|CI263779.1|CI263779
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTAC------AAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|38472703|gb|CF956835.1|CF956835
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGT----                         --CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88240099|gb|CI239261.1|CI239261
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGT----                         --CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|87013474|gb|CI267175.1|CI267175
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88241693|gb|CI241542.1|CI241542
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGT----                         --CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|87018749|gb|CI254457.1|CI254457
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGT----                         --CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86522577|gb|CI162783.1|CI162783
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGT----                         --CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|87025174|gb|CI265739.1|CI265739
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88243737|gb|CI242859.1|CI242859
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGT----                         --CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86507626|gb|CI150259.1|CI150259
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTAC------AAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|117247693|gb|CT848586.1|CT848586
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGT----                         --CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86545808|gb|CI186014.1|CI186014
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTAC------AAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|29680631|gb|CB676906.1|CB676906
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGT----                         --CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88203908|gb|CI203757.1|CI203757
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88205075|gb|CI204924.1|CI204924
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|29680632|gb|CB676907.1|CB676907
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGT----                         --CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|87028385|gb|CI263727.1|CI263727
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTAC------AAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86597557|gb|CI282681.1|CI282681
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTAC------AAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86509682|gb|CI152315.1|CI152315
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTAC------AAAG                         GTCCTGGTGTCTATTCCTCGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86506792|gb|CI149425.1|CI149425
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88204552|gb|CI204401.1|CI204401
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTAC------AAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88384832|gb|CI559100.1|CI559100
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTAC------AAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|88977533|gb|CI025269.1|CI025269
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGT----                         --CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|87031417|gb|CI261791.1|CI261791
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGT----                         --CCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
EST: gi|86592601|gb|CI253282.1|CI253282
EST:     CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAG                         GTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG
genomic: CGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAG

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: 50 (upstream exon), 75 (downstream exon)
Score: 16

GTCTTCGAGGTCGGCTCCGTCTCCGCCAAGTTCCCCGCCCGCCACTTCAACGCCAGCCTCGAGTGCCCCGCCAAAGCCGACTCTTAGTACAAAGGTAAAGgtactagcaa ... cctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAGGCTTTCAGTGTTCTCTGTTTCTTCGCACCTGTCTGTAATTATTCGTGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttctgttaaatggattaacgaagaatctcatcgttttttttccctttttcagGTCCTGGTGTCTATTCCTTGATATGGCATCATGAAGCGGCTTAGGCTTCAGGCTTTCAGTGTTCTCTGTTTCTTCGCACCTGTCTGTAATTATTCGTGTA
               gattaac  putative branch site (score: 16)
                            tctcatcgtttttttt  putative PPT
                                    tttttttt  TA-rich tract