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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACGCAGCCGGCGGCTTAGGGTTTTGTAGCTGTCGCCGATCCAAGgtacgcagcctccgagcgccgcctctctctcacacacacgagcgcttccttactcgagatctctcgcgcccctctccgcttcgattctctgtttgttgatcgattttggtttgttccgtcgccttcgccgcag

Basic information

species Oryza sativa
transcript LOC_Os01g62350.1
intron # 1
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|66915881|gb|CX102729.1|CX102729
EST:     CGGCGGCTTAGGGTTTTGTAGCTGTCGCCGATCCAAG                         GTCCGAGGAGCGAGGAGGAGATCCGCCATGGCGCCGCCGCAGCCCAAGTCG
genomic: CGGCGGCTTAGGGTTTTGTAGCTGTCGCCGATCCAAGgtacgcagcc ... ttcgccgcagGTCCGAGGAGCGAGGAGGAGATCCGCCATGGCGCCGCCGCAGCCCAAGTCG
EST: gi|86529019|gb|CI169225.1|CI169225
EST:     GCTGTCGCCGATCCAAG                         GTCCGAGGAGCGAGGAGGAGATCCGCCATGGCGCCGCCGCAGCCCAAGTCG
genomic: GCTGTCGCCGATCCAAGgtacgcagcc ... ttcgccgcagGTCCGAGGAGCGAGGAGGAGATCCGCCATGGCGCCGCCGCAGCCCAAGTCG
EST: gi|88315091|gb|CI610150.1|CI610150
EST:     GGACGCAGCCGGCGGCTTAGGGTTTTGTAGCTGTCGCCGATCCAAG                         GTCCGAGGAGCGAGGAGGAGATCCGCCATGGCGCCGCCGCAGCCCAAGTCG
genomic: GGACGCAGCCGGCGGCTTAGGGTTTTGTAGCTGTCGCCGATCCAAGgtacgcagcc ... ttcgccgcagGTCCGAGGAGCGAGGAGGAGATCCGCCATGGCGCCGCCGCAGCCCAAGTCG
EST: gi|87016064|gb|CI281807.1|CI281807
EST:     CCGGCGGCTTAGGGTTTTGTAGCTGTCGCCGATCCAAG                         GTCCGAGGAGCGAGGAGGAGATCCGCCATGGCGCCGCCGCAGCCCAAGTCG
genomic: CCGGCGGCTTAGGGTTTTGTAGCTGTCGCCGATCCAAGgtacgcagcc ... ttcgccgcagGTCCGAGGAGCGAGGAGGAGATCCGCCATGGCGCCGCCGCAGCCCAAGTCG
EST: gi|88369733|gb|CI680402.1|CI680402
EST:     GGACGCAGCCGGCGGCTTAGGGTTTTGTAGCTGTCGCCGATCCAAG                         GTCCGAGGAGCGAGGAGGAGATCCGCCATGGCGCCGCCGCAGCCCAAGTCG
genomic: GGACGCAGCCGGCGGCTTAGGGTTTTGTAGCTGTCGCCGATCCAAGgtacgcagcc ... ttcgccgcagGTCCGAGGAGCGAGGAGGAGATCCGCCATGGCGCCGCCGCAGCCCAAGTCG
EST: gi|58594171|gb|CF992479.1|CF992479
EST:     GGCGGCTTAGGG-TTTGTAGCTGTCGCCGATCCAAG                         GTCCGAGGAGCGAGGAGGAGATCCGCCATGGCGCCGCCGCAGCCCAAGTCG
genomic: GGCGGCTTAGGGTTTTGTAGCTGTCGCCGATCCAAGgtacgcagcc ... ttcgccgcagGTCCGAGGAGCGAGGAGGAGATCCGCCATGGCGCCGCCGCAGCCCAAGTCG

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), 75 (downstream exon)
Score: 55

GGACGCAGCCGGCGGCTTAGGGTTTTGTAGCTGTCGCCGATCCAAGgtacgcagcc ... ttcgccgcagGTCCGAGGAGCGAGGAGGAGATCCGCCATGGCGCCGCCGCAGCCCAAGTCGGGGCTCTTCGTCGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGC




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