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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaagtttcgtttttataccctcaccctcaattgggatgattaggaggttgaatgttaattaacatggtgcctgtcttcagGGTATTGCTCTGATTGTTACTGTAATCCAAATTGTTAGGATACCTAACCTCAAG

Basic information

species Oryza sativa
transcript LOC_Os02g57710.1
intron # 8
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|300216268|gb|HO088053.1|HO088053
EST:     GGGCTGTTTATCGCCGGATGACCTATGCTTGGATTGGGCAAGATATTCTT                         GGTATTGCTCTGATTGTTACTGTAATCCAAATTGTTAGGATACCTAACCTC
genomic: GGGCTGTTTATCGCCGGATGACCTATGCTTGGATTGGGCAAGATATTCTTgtaagtgaag ... ctgtcttcagGGTATTGCTCTGATTGTTACTGTAATCCAAATTGTTAGGATACCTAACCTC




















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), 54 (downstream exon)
Score: 52

ATACCTTACAATCGCAGTCTGTCCATTTTGCATTGTGTTTGCTGTTATATGGGCTGTTTATCGCCGGATGACCTATGCTTGGATTGGGCAAGATATTCTTgtaagtgaag ... ctgtcttcagGGTATTGCTCTGATTGTTACTGTAATCCAAATTGTTAGGATACCTAACCTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcaattgggatgattaggaggttgaatgttaattaacatggtgcctgtcttcagGGTATTGCTCTGATTGTTACTGTAATCCAAATTGTTAGGATACCTAACCTCAAG
                               aattaac  putative branch site (score: 52)
                                            cctgtcttc  putative PPT
                      ttgaatgttaattaa  TA-rich tract