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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAAAAGTCATGACATAGAAGAAGATATAGCTGATGAGCGGCTACAGTTTTGGATAGAACAAGGCAATCATCCAGTTTCTACGATCGATATCATAGAAGgtaatctcctctctgaacaatgatgaaactcttgtctcaaagtctgccatcctttgcactattcgttcaaagtttgaaatcatatacttctcgttttgactgtcttgtacaaaatttaccggctaaattgcttactttatctgatgcttttcttgtttgcaaaattatgtaaacaag

Basic information

species Oryza sativa
transcript LOC_Os05g05580.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g05580.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G017856_T01 (Zea mays), 5'ss of exon 1
GCCAAAAGTCATGACATAGAAGAAGATATAGCTGATGAGCGGCTACAGTTTTGGATAGAACAAGGCAATCATCCAGTTTCTACGATCGATATCATAGAAGgtaa--tctcctc-tctgaacaatgatgaaactcttgtctcaaagtctgccatcctttgcactattcgttcaaagtttgaaatcatatacttctcgttttgactgtcttgtacaaaatttaccggctaaattgcttactttatctgatgcttttcttgtttgcaaaattatgtaaacaag
|| |||| |||  ||||||||||||||||||||||||||  ||||||||||||||||||||||  |||| | |||||| |||||| |||  |  |||||||||   | || || ||    |    ||  ||   |   || | |||    || | |  |  || ||| ||       || || ||| ||                                                                                           
GCGAAAAATCACAACATAGAAGAAGATATAGCTGATGAGAAGCTACAGTTTTGGATAGAACAAATCAATTACCCAGTTACTACGAGCGAAGTAGTAGAAGgtagattatcttcatccattcggatattgaaacatgaactaacagtaaaacaccat--gatcttttccttttcctcctgcaaacatgtaaaaaag-------------------------------------------------------------------------------------
















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|88851230|gb|CI404282.1|CI404282
EST:     TTGGATAGAACAAGGCAATCATCCAGTTTCTACGATCGATATCATAGAAG                         TTGAGAGAGGACTTACTGAGCTGAGGAAGCTGGGAATGGAGTTTCAGCTGT
genomic: TTGGATAGAACAAGGCAATCATCCAGTTTCTACGATCGATATCATAGAAGgtaatctcct ... tgtaaacaagTTGAGAGAGGACTTACTGAGCTGAGGAAGCTGGGAATCGAGTCTCAGCTGT
EST: gi|88283553|gb|CI404999.1|CI404999
EST:     TTGGATAGAACAAGGCAATCATCCAGTTTGTACGATCGATATCATAGAAG                         TTGAGAGAGGACTTACTNAGCTGAGGAAGCTGGGAATCGAGTCTCAGCTGT
genomic: TTGGATAGAACAAGGCAATCATCCAGTTTCTACGATCGATATCATAGAAGgtaatctcct ... tgtaaacaagTTGAGAGAGGACTTACTGAGCTGAGGAAGCTGGGAATCGAGTCTCAGCTGT
EST: gi|88491687|gb|CI428959.1|CI428959
EST:     TTGGATAGAACAAGGCAATCATCCAGTTTCTACGATCGATATCATAGAAG                         TTGAGAGAGGACTTACTGAGCTGAGGAAGCTGGGAATCGAGTCTCAGCTGT
genomic: TTGGATAGAACAAGGCAATCATCCAGTTTCTACGATCGATATCATAGAAGgtaatctcct ... tgtaaacaagTTGAGAGAGGACTTACTGAGCTGAGGAAGCTGGGAATCGAGTCTCAGCTGT

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: 53 (upstream exon), 36 (downstream exon)
Score: 2

GCCAAAAGTCATGACATAGAAGAAGATATAGCTGATGAGCGGCTACAGTTTTGGATAGAACAAGGCAATCATCCAGTTTCTACGATCGATATCATAGAAGgtaatctcct ... tgtaaacaagTTGAGAGAGGACTTACTGAGCTGAGGAAGCTGGGAATCGAGTCTCAGCTGTGGGAATCGACGAGGAGATCTCTCGACGATGACTTTAGCAATCACGGGAG




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