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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccctaagttctattcatgaagttacacttgagactagttcaggtctttttgtatatttgttttatatcattaactaagtgttactcgttctttttgcagGCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACG

Basic information

species Oryza sativa
transcript LOC_Os01g28680.3
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|33674946|gb|CF303185.1|CF303185
EST:     TACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTA                         GCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGC
genomic: TACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTAgtaagactct ... ctttttgcagGCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGC
EST: gi|33795075|gb|CF323413.1|CF323413
EST:     TACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTA                         GCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGC
genomic: TACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTAgtaagactct ... ctttttgcagGCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGC
EST: gi|29612829|gb|CB617842.1|CB617842
EST:     TACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTA                         GCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGC
genomic: TACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTAgtaagactct ... ctttttgcagGCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGC
EST: gi|29688485|gb|CB684760.1|CB684760
EST:     TACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTA                         GCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGC
genomic: TACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTAgtaagactct ... ctttttgcagGCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGC
EST: gi|33675917|gb|CF304156.1|CF304156
EST:     TACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTA                         GCTTATTCCAGTCTGTCACCTATCGTTCATATG
genomic: TACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTAgtaagactct ... ctttttgcagGCTTATTCCAGTCTGTCACCTATCGTTCATATG
EST: gi|33676806|gb|CF305045.1|CF305045
EST:     TACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTA                         GCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGC
genomic: TACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTAgtaagactct ... ctttttgcagGCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGC
EST: gi|33676175|gb|CF304414.1|CF304414
EST:     TACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTA                         GCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGC
genomic: TACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTAgtaagactct ... ctttttgcagGCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGC
EST: gi|33693127|gb|CF321366.1|CF321366
EST:     TACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTA                         GCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGC
genomic: TACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTAgtaagactct ... ctttttgcagGCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGC

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: 73 (upstream exon), 75 (downstream exon)
Score: 56

CAATGCTGAGAAAAAGTGGACGATACATAAGGACATAACCTGCAAAAAGCTACGTTGGACAGTTTCAGATATTGCTCTTTCACCTGATCAACGATACCTAgtaagactct ... ctttttgcagGCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttgtatatttgttttatatcattaactaagtgttactcgttctttttgcagGCTTATTCCAGTCTGTCACCTATCGTTCATATGGTAGATATCCAGAATGGCATGAGAGAATCACATGCCAATATTACG
                       cattaac  putative branch site (score: 56)
                                    ttactcgttcttttt  putative PPT
     tgtatatttgttttat  TA-rich tract