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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgccggcctctctagctctgcttccatccagcccgatactcctgatgcgctcatcgattttgctgctgtttccgaaacgcagGCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG

Basic information

species Oryza sativa
transcript LOC_Os02g42520.2
intron # 2
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|25797193|gb|CA753154.1|CA753154
EST:     TCGTCTCCACCTCCATCTGCCGCAGTGACGTCACCCAGTGGCAATCCACG                         GCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG
genomic: TCGTCTCCACCTCCATCTGCCGCAGTGACGTCACCCAGTGGCAATCCACGgtacgccggc ... cgaaacgcagGCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG
EST: gi|88357025|gb|CI620913.1|CI620913
EST:     TCGTCTCCACCTCCATCTGCCGCAGTGACGTCACCCAGTGGCAATCCACG                         GCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG
genomic: TCGTCTCCACCTCCATCTGCCGCAGTGACGTCACCCAGTGGCAATCCACGgtacgccggc ... cgaaacgcagGCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG
EST: gi|88372773|gb|CI612701.1|CI612701
EST:     TCGTCTCCACCTCCATCTGCCGCAGTGACGTCACCCAGTGGCAATCCACG                         GCTCAAACCGATCTGTTCCCCAG
genomic: TCGTCTCCACCTCCATCTGCCGCAGTGACGTCACCCAGTGGCAATCCACGgtacgccggc ... cgaaacgcagGCTCAAACCGATCTGTTCCCCAG
EST: gi|58602019|gb|CK012547.1|CK012547
EST:     TCGTCTCCACCTCCATCTGCCGCAGTGACGTCACCCAGTGGCAATCCACG                         GCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG
genomic: TCGTCTCCACCTCCATCTGCCGCAGTGACGTCACCCAGTGGCAATCCACGgtacgccggc ... cgaaacgcagGCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG
EST: gi|88425441|gb|CI567161.1|CI567161
EST:     TCGTCTCCAACTCCATCTGCCGCAGTGACGTCACCCAGTGGCAATCCACG                         GCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG
genomic: TCGTCTCCACCTCCATCTGCCGCAGTGACGTCACCCAGTGGCAATCCACGgtacgccggc ... cgaaacgcagGCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG
EST: gi|88449400|gb|CI582272.1|CI582272
EST:     TCGTCTCCACCTCCATCTGCCGCAGTGACGTCACCCAGTGGCAATCCACG                         GCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG
genomic: TCGTCTCCACCTCCATCTGCCGCAGTGACGTCACCCAGTGGCAATCCACGgtacgccggc ... cgaaacgcagGCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG
EST: gi|58658973|gb|CK047653.1|CK047653
EST:     TCGTCTCCACCTCGGTCTGCCGCAGTGACGTCACCCAGTGGCAATCCACG                         GCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG
genomic: TCGTCTCCACCTCCATCTGCCGCAGTGACGTCACCCAGTGGCAATCCACGgtacgccggc ... cgaaacgcagGCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG
EST: gi|29617893|gb|CB622905.1|CB622905
EST:     TCGTCTCCACCTCCATCTGCCGCAGTGACGTCACCCAGTGGCAATCCACG                         GCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG
genomic: TCGTCTCCACCTCCATCTGCCGCAGTGACGTCACCCAGTGGCAATCCACGgtacgccggc ... cgaaacgcagGCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG

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: 40 (upstream exon), 71 (downstream exon)
Score: 4

GGAGGAGGTGGAGGTGGCGCCGCCGGAGGCCATGGAGATCCGCGTCAAGGTCGTCTCCACCTCCATCTGCCGCAGTGACGTCACCCAGTGGCAATCCACGgtacgccggc ... cgaaacgcagGCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagcccgatactcctgatgcgctcatcgattttgctgctgtttccgaaacgcagGCTCAAACCGATCTGTTCCCCAGAATTTTCGGGCACGAAGCATCCGG
            tcctgat  putative branch site (score: 4)
                                      ctgtttcc  putative PPT
                             atttt  TA-rich tract