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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acataaccacaagccttttatcttctacatagtacctagcaacttatatgcagcaaccattttgatatttcccctaacgtacctatttccgattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACACTCTCAGATGCCACTCCCAATGGCACATGATCAGCTGCTTTTCATCAGG

Basic information

species Oryza sativa
transcript LOC_Os01g63060.1
intron # 11
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|38475796|gb|CF959929.1|CF959929
EST:     AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGG                         CGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
genomic: AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
EST: gi|89166101|gb|CI103191.1|CI103191
EST:     ACTGTCGATTCTACTGATCGG                         CGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
genomic: ACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
EST: gi|87004430|gb|CI298962.1|CI298962
EST:     GAAACACTGTCGATTCTACTGATCGG                         CGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
genomic: GAAACACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
EST: gi|300215948|gb|HO088574.1|HO088574
EST:     AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGG                         CGGNCA-CGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACAC
genomic: AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGG-CAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACAC
EST: gi|8528209|gb|AU093024.1|AU093024
EST:     AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGG                         CGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
genomic: AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
EST: gi|33796561|gb|CF324148.1|CF324148
EST:     AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGG                         CGGCAACGTGTGCAGATGAACGGAAAAACATGGCGAGGACATCAACCCCAC
genomic: AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGGCAACGTGTGCAGATGAACGG-AAAACATGGCGAGGACATCAA--CCAC
EST: gi|88219746|gb|CI219306.1|CI219306
EST:     TAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGG                         CGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
genomic: TAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
EST: gi|29646377|gb|CB651384.1|CB651384
EST:     AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGG                         CGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
genomic: AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA

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: 72 (upstream exon), 69 (downstream exon)
Score: 17

CAGAACAAAGGAAGAGCTCCATAAACTAGAGAAGGATTGCAAGATGAAGGAAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACACTCTCAGATGCCACTCCCAATGGCACATGATCAGCTGCTTTTCATCAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgcagcaaccattttgatatttcccctaacgtacctatttccgattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACACTCTCAGATGCCACTCCCAATGGCACATGATCAGCTGCTTTTCATCAGG
                          ccctaac  putative branch site (score: 17)
             attttgatattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acataaccacaagccttttatcttctacatagtacctagcaacttatatgcagcaaccattttgatatttcccctaacgtacctatttccgattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACACTCTCAGATGCCACTCCCAATGGCACATGATCAGCTGCTTTTCATCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - -cacaagc
- - - - - - - - - - - - - - - - - - - - - - - - tgcagca