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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaaatggattccaataattgcttttcagggggaaaaatggacatgttgatgaatctcagtactaatcacttggcaaattcagGGTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGAAGAGCGGGAAAGCTACCGGGAGACACGACTTCTACGTTAAAAGCTTGGT

Basic information

species Oryza sativa
transcript LOC_Os08g19650.1
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|33662235|gb|CF293202.1|CF293202
EST:     GATCCCTAATGGAGCGTGTCCGTCAAGAGCTAAAGCATGAACTAAAGCAG                         GGTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGA
genomic: GATCCCTAATGGAGCGTGTCCGTCAAGAGCTAAAGCATGAACTAAAGCAGgtttgaaatg ... gcaaattcagGGTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGA
EST: gi|29685658|gb|CB681933.1|CB681933
EST:     GATCCCTAATGGAGCGTGTCCGTCAAGAGCTAAAGCATGAACTAAAGCAG                         GGTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGA
genomic: GATCCCTAATGGAGCGTGTCCGTCAAGAGCTAAAGCATGAACTAAAGCAGgtttgaaatg ... gcaaattcagGGTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGA
EST: gi|29639210|gb|CB644219.1|CB644219
EST:     GATCCCTAATGGAGCGTGTCCGTCAAGAGCTAAAGCATGAACTAAAGCAG                         GGTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGA
genomic: GATCCCTAATGGAGCGTGTCCGTCAAGAGCTAAAGCATGAACTAAAGCAGgtttgaaatg ... gcaaattcagGGTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGA
EST: gi|58687578|gb|CK076265.1|CK076265
EST:     CCCTAATGGAGCGTGT-CGTCAAGAGCTAAAGCATGAACTAAAGCAG                         GCTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGA
genomic: CCCTAATGGAGCGTGTCCGTCAAGAGCTAAAGCATGAACTAAAGCAGgtttgaaatg ... gcaaattcagGGTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGA
EST: gi|38469479|gb|CF953610.1|CF953610
EST:     GATCCCTAATGGAGCGTGTCCGTCAAGAGCTAAAGCATGAACTAAAGCAG                         GGTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGA
genomic: GATCCCTAATGGAGCGTGTCCGTCAAGAGCTAAAGCATGAACTAAAGCAGgtttgaaatg ... gcaaattcagGGTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGA
EST: gi|58589921|gb|CF988229.1|CF988229
EST:     GATCCCTAATGGAGCGTGTCCGTCAAGAGCTAAAGCATGAACTAAAGCAG                         GGTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGA
genomic: GATCCCTAATGGAGCGTGTCCGTCAAGAGCTAAAGCATGAACTAAAGCAGgtttgaaatg ... gcaaattcagGGTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGA
EST: gi|58689922|gb|CK078609.1|CK078609
EST:     GATCCCTAATGGAGCGTGTCCGTCAAGAGCTAAAGCATGAACTAAAGCAG                         GGTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGA
genomic: GATCCCTAATGGAGCGTGTCCGTCAAGAGCTAAAGCATGAACTAAAGCAGgtttgaaatg ... gcaaattcagGGTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGA

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: 74 (upstream exon), 74 (downstream exon)
Score: 25

CTTGGATGGAGCGGATAACATGGGTTTCGGCCTTCCCACAGAAAGCGAGCGATCCCTAATGGAGCGTGTCCGTCAAGAGCTAAAGCATGAACTAAAGCAGgtttgaaatg ... gcaaattcagGGTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGAAGAGCGGGAAAGCTACCGGGAGACACGACTTCTACGTTAAAAGCTTGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggggaaaaatggacatgttgatgaatctcagtactaatcacttggcaaattcagGGTTACAAAGAGAAGCTGATTGACATAAGAGAAGAAATTCTTCGCAAGCGAAGAGCGGGAAAGCTACCGGGAGACACGACTTCTACGTTAAAAGCTTGGT
                                tactaat  putative branch site (score: 25)
     aaaaat  TA-rich tract