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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcgcaatacatctttcttttctactcgagaaatagcttactgagacctgtcatttttgggtcaggtgctaactggtaacagtgacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGATTTTCTGCTTTAGCTGTTTGGACATTCTTTTATCTTAATAATTGGGTAAT

Basic information

species Oryza sativa
transcript LOC_Os09g07830.3
intron # 13
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|42592163|gb|CK738649.1|CK738649
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTTGACATT                   
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAG-C-----C-TTgtaaggcgca ... gaca
EST: gi|42592163|gb|CK738649.1|CK738649
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTTGACATT                   
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAG-C-----C-TTgtaaggcgca ... gaca
EST: gi|42592163|gb|CK738649.1|CK738649
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTTGACATT                   
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAG-C-----C-TTgtaaggcgca ... gaca
EST: gi|42592163|gb|CK738649.1|CK738649
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTTGACATT                   
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAG-C-----C-TTgtaaggcgca ... gaca
EST: gi|42592163|gb|CK738649.1|CK738649
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTTGACATT                   
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAG-C-----C-TTgtaaggcgca ... gaca
EST: gi|88265504|gb|CI376406.1|CI376406
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTT                         GTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
EST: gi|88278180|gb|CI399180.1|CI399180
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTT                         GTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
EST: gi|88270104|gb|CI381402.1|CI381402
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTT                         GTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
EST: gi|88462858|gb|CI519770.1|CI519770
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTT                         GTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
EST: gi|88959704|gb|CI002314.1|CI002314
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTT                         GTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
EST: gi|88291122|gb|CI527512.1|CI527512
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTT                         GTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
EST: gi|86536502|gb|CI176708.1|CI176708
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTT                         GTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
EST: gi|88273759|gb|CI394165.1|CI394165
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTT                         GTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
EST: gi|86537651|gb|CI177857.1|CI177857
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTT                         GTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
EST: gi|88975140|gb|CI023391.1|CI023391
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTT                         GTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
EST: gi|88522268|gb|CI450014.1|CI450014
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTT                         GTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
EST: gi|88267020|gb|CI378955.1|CI378955
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTT                         GTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
EST: gi|88468140|gb|CI517599.1|CI517599
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTT                         GTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
EST: gi|88267537|gb|CI379472.1|CI379472
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTT                         CTGATCCATCTCCAGTTCTCCAGGACGGTTTGTGTACTCTAGTTTATTTGA
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACG-TTTGTGTACTCTAGTTTATTTGA
EST: gi|89198029|gb|CI117507.1|CI117507
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTT                         GTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
EST: gi|88295383|gb|CI527746.1|CI527746
EST:     GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTT                         GTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT
genomic: GGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGAT

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), 74 (downstream exon)
Score: 46

GTTCTTAGGGAGAAAGGTGGCAAAATCGGAGTTGCTGGTGTTTGCAATGGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAGCCTTgtaaggcgca ... gacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGATTTTCTGCTTTAGCTGTTTGGACATTCTTTTATCTTAATAATTGGGTAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgagacctgtcatttttgggtcaggtgctaactggtaacagtgacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGATTTTCTGCTTTAGCTGTTTGGACATTCTTTTATCTTAATAATTGGGTAAT
            tcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggcgcaatacatctttcttttctactcgagaaatagcttactgagacctgtcatttttgggtcaggtgctaactggtaacagtgacattgcagGTGATCCATCTCCAGTTCTCCAGGACGTTTGTGTACTCTAGTTTATTTGATTTTCTGCTTTAGCTGTTTGGACATTCTTTTATCTTAATAATTGGGTAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT