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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaatcttgtatttcatatgttgctgaacaaaatctaagttctgtttcttgaagcctttgtttgtttgtgatacagCCACACTCTCCAGATTACAGGCCATATATTGGTCCAATCTATAAGGCTATCTTGGCCCGCTTGGCAAATCAGGATCAGGATCAGGATCAG

Basic information

species Oryza sativa
transcript LOC_Os02g07340.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G168629_T02 (Zea mays), 3'ss of exon 15
gtcaatcttgtatttcatatgttgctgaacaaaat----ctaagttctgtttcttgaa--gcctttgtttgtttgtgatacagCCACACTCTCCAGATTACAGGCCATATATTGGTCCAATCTATAAGGCTATCTTGGCCCGCTTGGCAAATCAGGATCAGGATCAGGATCAG----------
|||| | ||||||| |||   |||| ||    |||    ||     || ||| || |      ||||||  |||||| | ||| ||  |||    ||||  | |||||| ||||||||||||||||| || ||  |||  || ||||| ||||| ||||||||||||| |  |          
gtca-tattgtattccatgccttgcggacatgaattaccctgttacctttttatttatttatttttgttattttgtggtgcagACAACCTCAGTTGATTTTAAGCCATACATTGGTCCAATCTATAATGCAATACTGGGACGTTTGGCCAATCAAGATCAGGATCAGGTTTGGCAAAATTCTC
















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: 66 (upstream exon), 44 (downstream exon)
Score: 7

CCCAATATTGTCTGCTATTGGAGACAGATATGACAAGGTCACCGCTGAGGCTTTAAGAGTCTGCGAAGAGCTAGTTCGTGTACTTCGTCCAAATTCTGAGgtcaatcttg ... tgtgatacagCCACACTCTCCAGATTACAGGCCATATATTGGTCCAATCTATAAGGCTATCTTGGCCCGCTTGGCAAATCAGGATCAGGATCAGGATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgaacaaaatctaagttctgtttcttgaagcctttgtttgtttgtgatacagCCACACTCTCCAGATTACAGGCCATATATTGGTCCAATCTATAAGGCTATCTTGGCCCGCTTGGCAAATCAGGATCAGGATCAGGATCAG
                                       tttgttt  CT-rich tract
        aaaatctaa  TA-rich tract