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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGACCCACGGCATAGATATGGTCACAATCTGCATTTCTACTATGATGTTTGGTGCCAAAGCCAGGCCGGCCAGCCATTCTTCTACTGgtaagaagttggttgtgttttgtgtgtttgcatttgcaaagtatgttgttggaagaaatgggttggatgtctgtgacacaagagatttgcaggcagagtaatagattcagtgttgcactcttatctcagaaatttcagtgagtggtttggttgtgcattgaattcaataatctttatgcatatgtag

Basic information

species Oryza sativa
transcript LOC_Os12g05420.1
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|88385913|gb|CI568581.1|CI568581
EST:     TACTATGATGTTTGGTGCCAAAGCCAGGCCGGCCAGCCATTCTTCTACTG                         GCTTGATATTGGGGAAGGAAAAGATGTTGACCTTCCTGAGTGTCCC-GAGC
genomic: TACTATGATGTTTGGTGCCAAAGCCAGGCCGGCCAGCCATTCTTCTACTGgtaagaagtt ... gcatatgtagGCTTGATATTGGGGAAGGAAAAGATGTTGACCTTCCTGAGTGTCCCAGAGC
EST: gi|29688635|gb|CB684910.1|CB684910
EST:     TACTATGATGTTTGGTGCCAAAGCCAGGCCGGCCAGCCATTCTTCTACTG                         GCTTGATATTGGGGAAGGAAAAGATGTTGACCTTCCTGAGTGTCCCAGAGC
genomic: TACTATGATGTTTGGTGCCAAAGCCAGGCCGGCCAGCCATTCTTCTACTGgtaagaagtt ... gcatatgtagGCTTGATATTGGGGAAGGAAAAGATGTTGACCTTCCTGAGTGTCCCAGAGC
EST: gi|33797243|gb|CF324484.1|CF324484
EST:     TACTATGATGTTTGGTGCCAAAGCCAGGCCGGCCAGCCATTCTTCTACTG                         GCTTGANTATTGGGGAAGGAAAAGATGTTGACCTTCCTGAGTGTCCCAGAG
genomic: TACTATGATGTTTGGTGCCAAAGCCAGGCCGGCCAGCCATTCTTCTACTGgtaagaagtt ... gcatatgtagGCTTGA-TATTGGGGAAGGAAAAGATGTTGACCTTCCTGAGTGTCCCAGAG

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: 73 (upstream exon), 66 (downstream exon)
Score: 32

ATTGACCCACGGCATAGATATGGTCACAATCTGCATTTCTACTATGATGTTTGGTGCCAAAGCCAGGCCGGCCAGCCATTCTTCTACTGgtaagaagtt ... gcatatgtagGCTTGATATTGGGGAAGGAAAAGATGTTGACCTTCCTGAGTGTCCCAGAGCTCGCCTGAAGAAGCAATGCATAAAATATCTTGGTCCG




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