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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggctgatgcatcaactttactcccaatcatctttttccgttccctacttcatgttattcacctacattggtcttactggcatgcctgaacttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCACCGTGATGATAGTAAAAAAGCCGAAGCACAAGCACTGAGTCCATGAGCGG

Basic information

species Oryza sativa
transcript LOC_Os12g36640.2
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|88981775|gb|CI027353.1|CI027353
EST:     CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
genomic: CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
EST: gi|88508997|gb|CI436503.1|CI436503
EST:     CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
genomic: CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
EST: gi|88538240|gb|CI467253.1|CI467253
EST:     GCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
genomic: GCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
EST: gi|89168596|gb|CI038448.1|CI038448
EST:     CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
genomic: CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
EST: gi|86424109|gb|CI062870.1|CI062870
EST:     CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
genomic: CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
EST: gi|29623326|gb|CB628337.1|CB628337
EST:     CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
genomic: CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
EST: gi|88480444|gb|CI417715.1|CI417715
EST:     CAGGCGGAGATNTTGGTTGTCGGAACCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGAGTACTGTTCTCATCATGCGCACTGCAC
genomic: CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
EST: gi|88291994|gb|CI532586.1|CI532586
EST:     CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
genomic: CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
EST: gi|218498665|gb|FG952674.1|FG952674
EST:     CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
genomic: CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
EST: gi|58031113|gb|CX728656.1|CX728656
EST:     CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
genomic: CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
EST: gi|88477005|gb|CI414276.1|CI414276
EST:     CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
genomic: CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
EST: gi|8860142|gb|AU097460.1|AU097460
EST:     CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
genomic: CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
EST: gi|88293088|gb|CI512853.1|CI512853
EST:     TGGTTTTCGGAAGCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGACTACTNTTCTCATCATGCGCACTGCAC
genomic: TGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
EST: gi|218783373|gb|GE329425.1|GE329425
EST:     CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
genomic: CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
EST: gi|94362829|gb|CI052990.1|CI052990
EST:     CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
genomic: CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
EST: gi|88324041|gb|CI561450.1|CI561450
EST:     TGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGAGTACTGTTCTCATCATGCGCACTGCAC
genomic: TGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
EST: gi|29686559|gb|CB682834.1|CB682834
EST:     CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACG                         AGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC
genomic: CAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCAC

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: 68 (upstream exon), 23 (downstream exon)
Score: 4

TGCTGGAAGGGGATGCCAGGAATGTTCTTTGTGAGTCTGTTGAGAGGCATCAGGCGGAGATGTTGGTTGTCGGAAGCCATGGCTATGGAGCAATTAAACGgtattgccat ... ttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCACCGTGATGATAGTAAAAAAGCCGAAGCACAAGCACTGAGTCCATGAGCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttcatgttattcacctacattggtcttactggcatgcctgaacttccctgcagAGCTGTTCTTGGAAGCGTGAGTGACTACTGTTCTCATCATGCGCACTGCACCGTGATGATAGTAAAAAAGCCGAAGCACAAGCACTGAGTCCATGAGCGG
                        gtcttac  putative branch site (score: 4)
                                            cttccctgc  putative PPT
     atgttatt  TA-rich tract