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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacaatccctctcctactttatagaagcatatgccatagaaatcctaaatatatgtgctctaaatgcatatatttgctgtgtgcagGCTCATCCATATTTCAATCCAGTGAGAAGCACTTAAAACGGCAGGAAGAGTGCCCAATAGTGGTATGCGGCATATTTGACAATTTTTGCTACGGTGTCAA

Basic information

species Oryza sativa
transcript LOC_Os03g55490.1
intron # 9
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|58030601|gb|CX728144.1|CX728144
EST:     TTGGAAGACATAATAGGAAGCCATGGTCAATGTTTGTTAACTCGGGGAACAGACACCTAGCAAGCCCTGAG
genomic: TTGGAAGACATAATAGGAAGCCATGGTCAATGTTTGTTAACTCGGGGAACAGACACCTAGCAAGCCCTGAG
EST: gi|29644831|gb|CB649838.1|CB649838
EST:     TTGGAAGACATAATAGGAAGCCATGGTCAATGTTTGTTAACTCGGGGAACAGACACCTAGCAAGCCCTGAG
genomic: TTGGAAGACATAATAGGAAGCCATGGTCAATGTTTGTTAACTCGGGGAACAGACACCTAGCAAGCCCTGAG
EST: gi|29643382|gb|CB648389.1|CB648389
EST:     TTGGAAGACATAATAGGAAGCCATGGTCAATGTTTGTTAACTCGGGGAACAGACACCTAGCAAGCCCTGAG
genomic: TTGGAAGACATAATAGGAAGCCATGGTCAATGTTTGTTAACTCGGGGAACAGACACCTAGCAAGCCCTGAG
EST: gi|66915335|gb|CX102183.1|CX102183
EST:     TTGGAAGACATAATAGGAAGCCATGGTCAATGTTTGTTAACTCGGGGAACAGACACCTAGCAAGCCCTGAG
genomic: TTGGAAGACATAATAGGAAGCCATGGTCAATGTTTGTTAACTCGGGGAACAGACACCTAGCAAGCCCTGAG
EST: gi|86595025|gb|CI260264.1|CI260264
EST:     TTGGAAGACATAATAGGAAGCCATGGTCAATGTTTGTTAACTCGGGGAACAGACACCTAGCAAGCCCTGAG
genomic: TTGGAAGACATAATAGGAAGCCATGGTCAATGTTTGTTAACTCGGGGAACAGACACCTAGCAAGCCCTGAG
EST: gi|88521841|gb|CI449006.1|CI449006
EST:     GGTTGCTTCGCTACGATCACCAGGAAAGGCCTACAGCAAAGGAAGCCATG                         GCTCATCCATATTTCAATCCAGTGAGAAGCACTTAAAACGGCAGGAAGAGT
genomic: GGTTGCTTCGCTACGATCACCAGGAAAGGCCTACAGCAAAGGAAGCCATGgtgacaatcc ... ctgtgtgcagGCTCATCCATATTTCAATCCAGTGAGAAGCACTTAAAACGGCAGGAAGAGT
EST: gi|88322225|gb|CI537808.1|CI537808
EST:     GACATAATAGGAAGCCATGGTCAATNTTTGTTAACTCGGGGAACAGACACCTAGCAAGCCCTGAG
genomic: GACATAATAGGAAGCCATGGTCAATGTTTGTTAACTCGGGGAACAGACACCTAGCAAGCCCTGAG

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: 69 (upstream exon), 70 (downstream exon)
Score: 20

GCTATTGATTTTGTAGACAGGTTGCTTCGCTACGATCACCAGGAAAGGCCTACAGCAAAGGAAGCCATGgtgacaatcc ... ctgtgtgcagGCTCATCCATATTTCAATCCAGTGAGAAGCACTTAAAACGGCAGGAAGAGTGCCCAATAGTGGTATGCGGCATATTTGACAATTTTTGCTACGGTGTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccatagaaatcctaaatatatgtgctctaaatgcatatatttgctgtgtgcagGCTCATCCATATTTCAATCCAGTGAGAAGCACTTAAAACGGCAGGAAGAGTGCCCAATAGTGGTATGCGGCATATTTGACAATTTTTGCTACGGTGTCAA
        aaatcctaaatatat  TA-rich tract