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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTGGACATCAGAATCTTTGAAACAGGGGAGTATGCCCTGgtgagtcacctgccacttcatttcttctgtatattttgtagatttggacttctgaatctcattcatatgtttggacag

Basic information

species Oryza sativa
transcript LOC_Os01g72950.1
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|86251685|gb|CI016974.1|CI016974
EST:     GTTTTGGACATCAGAATCTTTGAAACAGGGGAGTATGCCCTG                         ATCGCTTGGGTTGGTATCCCAACTCCACCGGCATGGCTGCCAACTTACATG
genomic: GTTTTGGACATCAGAATCTTTGAAACAGGGGAGTATGCCCTGgtgagtcacc ... gtttggacagATCGCTTGGGTTGGAATCCCAACTCCACCGGCATGGCTGCCAACTTACATG
EST: gi|88540852|gb|CI468926.1|CI468926
EST:     GACATCAGAATCTTTGAGAGCAGGGGAGTATGCCCTG                         ATCGCTTGGGTTGGAATCCCGACTCCACCGGCATGGCTGCCAACTTACATG
genomic: GACATCAGAATCTTTGA-AACAGGGGAGTATGCCCTGgtgagtcacc ... gtttggacagATCGCTTGGGTTGGAATCCCAACTCCACCGGCATGGCTGCCAACTTACATG
EST: gi|14981716|gb|BI306394.1|BI306394
EST:     GTTTTGGACATCAGAATCTTTGAAACAGGGGAGTATGCCCTG                         ATCGCTTGGGTTGGAATCCCAACTCCACCGGCATGGCTGCCAACTTACATG
genomic: GTTTTGGACATCAGAATCTTTGAAACAGGGGAGTATGCCCTGgtgagtcacc ... gtttggacagATCGCTTGGGTTGGAATCCCAACTCCACCGGCATGGCTGCCAACTTACATG
EST: gi|14981699|gb|BI306377.1|BI306377
EST:     GTTTTGGACATCAGAATCTTTGAAACAGGGGAGTATGCCCTG                         ATCGCTTGGGTTGGAATCCCAACTCCACCGGCATGGCTGCCAACTTACATG
genomic: GTTTTGGACATCAGAATCTTTGAAACAGGGGAGTATGCCCTGgtgagtcacc ... gtttggacagATCGCTTGGGTTGGAATCCCAACTCCACCGGCATGGCTGCCAACTTACATG

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: 42 (upstream exon), 60 (downstream exon)
Score: 30

GTTTTGGACATCAGAATCTTTGAAACAGGGGAGTATGCCCTGgtgagtcacc ... gtttggacagATCGCTTGGGTTGGAATCCCAACTCCACCGGCATGGCTGCCAACTTACATGCTCATCAAG




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