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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtattcatgcacatcaactggcattagacaatctcacattttgcctgcttaatttacacacaatcaaagcttaattctatgttaacatcaggattttgttgtgcctaagtaacacctcttttgctatggatagATGAATCGGAAGCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCTCAACACTCAGGTCAACCTCAATAAGGTTTTTGTCTATTCTCTTAATGTT

Basic information

species Oryza sativa
transcript LOC_Os01g28989.2
intron # 3
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|88511446|gb|CI438952.1|CI438952
EST:     TGCAGCGGCAAAATAAAAAGTGATAGCTGAAGGAAAATCTTGGATTCATG                         ATGAATCGGAAGCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCT
genomic: TGCAGCGGCAAAATAAAAAGTGATAGCTGAAGGAAAATCTTGGATTCATGgtagtattca ... ctatggatagATGAATCGGAAGCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCT
EST: gi|29683562|gb|CB679837.1|CB679837
EST:     TGCAGCGGCAAAATAAAAAGTGATAGCTGAAGGAAAATCTTGGATTCATG                         ATGAATCGGAAGCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCT
genomic: TGCAGCGGCAAAATAAAAAGTGATAGCTGAAGGAAAATCTTGGATTCATGgtagtattca ... ctatggatagATGAATCGGAAGCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCT
EST: gi|88479773|gb|CI417044.1|CI417044
EST:     TGCAGCGGCAAAATAAAAAGTGATAGCTGAAGGAAAATCTTGGATTCATG                         ATGAATCGGAAGCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCT
genomic: TGCAGCGGCAAAATAAAAAGTGATAGCTGAAGGAAAATCTTGGATTCATGgtagtattca ... ctatggatagATGAATCGGAAGCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCT
EST: gi|88504680|gb|CI432186.1|CI432186
EST:     TGCAGCGGCAAAATAAAAAGTGATAGCTGAAGGAAAATCTTGGATTCATG                         ATGAATCGGAAGCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCT
genomic: TGCAGCGGCAAAATAAAAAGTGATAGCTGAAGGAAAATCTTGGATTCATGgtagtattca ... ctatggatagATGAATCGGAAGCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCT
EST: gi|86862740|gb|CI331636.1|CI331636
EST:     TGCAGCGGCAAAATAAAAAGTGATAGCTGAAGGAAAATCTTGGATTCATG                         ATGAATCGGAAGCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCT
genomic: TGCAGCGGCAAAATAAAAAGTGATAGCTGAAGGAAAATCTTGGATTCATGgtagtattca ... ctatggatagATGAATCGGAAGCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCT

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: 64 (upstream exon), 60 (downstream exon)
Score: 21

CTTGGATTTTTATGATGAAATGGCTAGCTTCGGTAGCTGATTTAGAATTTTGCAGCGGCAAAATAAAAAGTGATAGCTGAAGGAAAATCTTGGATTCATGgtagtattca ... ctatggatagATGAATCGGAAGCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCTCAACACTCAGGTCAACCTCAATAAGGTTTTTGTCTATTCTCTTAATGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttaacatcaggattttgttgtgcctaagtaacacctcttttgctatggatagATGAATCGGAAGCAGCAAGGAAGCATATGTCCTTTGTCGTTTGATTGGCCTCAACACTCAGGTCAACCTCAATAAGGTTTTTGTCTATTCTCTTAATGTT
                            aagtaac  putative branch site (score: 21)
                                    cctcttttgct  CT-rich tract
              attttgtt  TA-rich tract