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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcgcattcccaattgcccctcattcttccatacacttccaactccattgggtgctcatctctgtttgtgcctgatgatgtttcagAGAGTCCCAATCTGGTGGAGATGGTATTGCTGGGCGTGCCCCGTCGCGTGGACGCTGTACGGCCTCGTCGTCTCCCAGTTCGGTGACATCGAGACGCCGA

Basic information

species Oryza sativa
transcript LOC_Os01g42380.1
intron # 20
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|58590285|gb|CF988593.1|CF988593
EST:     CGTTCTACGCCATCTGGAATCTCTTCTCCGGCTTCGTCATCCCCCGACCT                         AGAGTCCCAATCTGGTGGAGATGGTATTGCTGGGCGT
genomic: CGTTCTACGCCATCTGGAATCTCTTCTCCGGCTTCGTCATCCCCCGACCTgtaagtttcg ... gatgtttcagAGAGTCCCAATCTGGTGGAGATGGTATTGCTGGGCGT
EST: gi|86413662|gb|CI019247.1|CI019247
EST:     GCCATCTGGAATCTCTTCTCCGGCTTCGTCATCCCCCGACCT                         AGAGTCCCAATCTGGTGGAGATGGTATTGCTGGGCGTGCCCCGTCGCGTGG
genomic: GCCATCTGGAATCTCTTCTCCGGCTTCGTCATCCCCCGACCTgtaagtttcg ... gatgtttcagAGAGTCCCAATCTGGTGGAGATGGTATTGCTGGGCGTGCCCCGTCGCGTGG
EST: gi|86593970|gb|CI260199.1|CI260199
EST:     CGTTCTACGCCATCTGGAATCTCTTCTCCGGCTTCGTCATCCCCCGACCT                         AGAGTCCCAATCTGGTGGAGATGGTATTGCTGGGCGTGCCCCGTCGCGTGG
genomic: CGTTCTACGCCATCTGGAATCTCTTCTCCGGCTTCGTCATCCCCCGACCTgtaagtttcg ... gatgtttcagAGAGTCCCAATCTGGTGGAGATGGTATTGCTGGGCGTGCCCCGTCGCGTGG
EST: gi|86481874|gb|CI124507.1|CI124507
EST:     CGTTCTACGCCATCTGGAATCTCTTCTCCGGCTTCGTCATCCCCCGACCT                         AGAGTCCCAATCTGGTGGAGATGGTATTGCTGGGCGTGCCCCGTCGCGTGG
genomic: CGTTCTACGCCATCTGGAATCTCTTCTCCGGCTTCGTCATCCCCCGACCTgtaagtttcg ... gatgtttcagAGAGTCCCAATCTGGTGGAGATGGTATTGCTGGGCGTGCCCCGTCGCGTGG

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), 39 (downstream exon)
Score: 3

GGCGGTCGGCCTGACACCGAACTACCACATTGCCTCGATCGTCTCATCGGCGTTCTACGCCATCTGGAATCTCTTCTCCGGCTTCGTCATCCCCCGACCTgtaagtttcg ... gatgtttcagAGAGTCCCAATCTGGTGGAGATGGTATTGCTGGGCGTGCCCCGTCGCGTGGACGCTGTACGGCCTCGTCGTCTCCCAGTTCGGTGACATCGAGACGCCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacacttccaactccattgggtgctcatctctgtttgtgcctgatgatgtttcagAGAGTCCCAATCTGGTGGAGATGGTATTGCTGGGCGTGCCCCGTCGCGTGGACGCTGTACGGCCTCGTCGTCTCCCAGTTCGGTGACATCGAGACGCCGA
                                      gcctgat  putative branch site (score: 3)