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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcttaacaaagtctagtgttggaaggaatttgttactcactcactaacagggtgtcttctttccttgcttgttgcagGCTGCTGTACCAAGCCATCCAAAGACGCAACATTGAAGTGCATCGGGTCAAACCAGCCAATGCTCCTGATTTGTTGTCTTTTGTCAATGATATCGAGTTC

Basic information

species Oryza sativa
transcript LOC_Os01g01040.4
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|86850742|gb|CI309554.1|CI309554
EST:     GGTACGTGCTCAGTAGCTAGCTTGATACTCTTCGTTGGATTAGTCACTGT                         GCTGCTGTACCAAGCCATCCAAAGACGCAACATTGAAGTGCATCGGGTCAA
genomic: GGTACGTGCTCAGTAGCTAGCTTGATACTCTTCGTTGGATTAGTCACTGTgtaagtgctt ... cttgttgcagGCTGCTGTACCAAGCCATCCAAAGACGCAACATTGAAGTGCATCGGGTCAA
EST: gi|29616467|gb|CB621479.1|CB621479
EST:     GGTACGTGCTCAGTAGCTAGCTTGATACTCTTCGTTGGATTAGTCACTGT                         GCTGCTGTAC-AAGCCATCCAAAGACGCAACATTGAAGTGCATCGGGTCAA
genomic: GGTACGTGCTCAGTAGCTAGCTTGATACTCTTCGTTGGATTAGTCACTGTgtaagtgctt ... cttgttgcagGCTGCTGTACCAAGCCATCCAAAGACGCAACATTGAAGTGCATCGGGTCAA

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: 71 (upstream exon), 56 (downstream exon)
Score: 10

GATGACCAGCAAGTACTGAGGAAAAGAAAAACAGAGTTGGGTGGTACGTGCTCAGTAGCTAGCTTGATACTCTTCGTTGGATTAGTCACTGTgtaagtgctt ... cttgttgcagGCTGCTGTACCAAGCCATCCAAAGACGCAACATTGAAGTGCATCGGGTCAAACCAGCCAATGCTCCTGATTTGTTGTCTTTTGTCAATGATATCGAGTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggaatttgttactcactcactaacagggtgtcttctttccttgcttgttgcagGCTGCTGTACCAAGCCATCCAAAGACGCAACATTGAAGTGCATCGGGTCAAACCAGCCAATGCTCCTGATTTGTTGTCTTTTGTCAATGATATCGAGTTC
                   cactaac  putative branch site (score: 10)
                              tgtcttctttccttgc  putative PPT
     atttgtta  TA-rich tract