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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgccggggatcctaccatatgtatcacttcctcgattcttcattcagttatgacctaaagtatagttggcaataggaactcttggaattgaagagatgttgcagtttcgtcagttgtcttatgattagtttggtgaaattaacgatcttttccttttcacttggttagGATGATGATTTCGATGAGTCGGCTTATGTGCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g37770.1
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|218501991|gb|FG959119.1|FG959119
EST:     GCGGGCTCAGCACCACGGCTCGCTGCTTCCAGATCGTGCTCTCCCCTCAG                         GATGATGATTTCGATGAGTCGGCTTATGTGCCAG
genomic: GCGGGCTCAGCACCACGGCTCGCTGCTTCCAGATCGTGCTCTCCCCTCAGgtttgtgccg ... acttggttagGATGATGATTTCGATGAGTCGGCTTATGTGCCAG
EST: gi|66913764|gb|CX100612.1|CX100612
EST:     GCGGGCTCAGCACCACGGCTCGCTGCTTCCAGATCGTGCTCTCCCCTCAG                         GATGATGATTTCGATGAGTCGGCTTATGTGCCAG
genomic: GCGGGCTCAGCACCACGGCTCGCTGCTTCCAGATCGTGCTCTCCCCTCAGgtttgtgccg ... acttggttagGATGATGATTTCGATGAGTCGGCTTATGTGCCAG
EST: gi|29670376|gb|CB666651.1|CB666651
EST:     GCGGGCTCAGCACCACGGCTCGCTGCTTCCAGATCGTGCTCTCCCCTCAG                         GATGATGATTTCGATGAGTCGGCTTATGTGCCAG
genomic: GCGGGCTCAGCACCACGGCTCGCTGCTTCCAGATCGTGCTCTCCCCTCAGgtttgtgccg ... acttggttagGATGATGATTTCGATGAGTCGGCTTATGTGCCAG
EST: gi|32948343|gb|BP184915.1|BP184915
EST:     GCGGGCTCAGCACCACGGCTCGCTGCTTCCAGATCGTGCTCTCCCCTCAG                         GATGATGATTTCGATGAGTCGGCTTATGTGCCAG
genomic: GCGGGCTCAGCACCACGGCTCGCTGCTTCCAGATCGTGCTCTCCCCTCAGgtttgtgccg ... acttggttagGATGATGATTTCGATGAGTCGGCTTATGTGCCAG
EST: gi|88456108|gb|CI567674.1|CI567674
EST:     GCGGGCTCAGCACCACGGCTCGCTGCTTCCAGATCGTGCTCTCCCCTCAG                         GATGATGATTTCGATGAGTCGGCTTATGTGCCAG
genomic: GCGGGCTCAGCACCACGGCTCGCTGCTTCCAGATCGTGCTCTCCCCTCAGgtttgtgccg ... acttggttagGATGATGATTTCGATGAGTCGGCTTATGTGCCAG

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), 63 (downstream exon)
Score: 29

AGATCGACCCCAGCGAGAGCGGGCTCAGCACCACGGCTCGCTGCTTCCAGATCGTGCTCTCCCCTCAGgtttgtgccg ... acttggttagGATGATGATTTCGATGAGTCGGCTTATGTGCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcttatgattagtttggtgaaattaacgatcttttccttttcacttggttagGATGATGATTTCGATGAGTCGGCTTATGTGCCAG
                       aattaac  putative branch site (score: 29)
                                tcttttccttttcact  putative PPT
     ttatgatta  TA-rich tract