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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgactgctgtatttagtgtatctcctaagttgaaagtgtagtgaagaactttttagcatttttttaaagatactttttgctcgtgttgattttt...

Basic information

species Oryza sativa
transcript LOC_Os02g11820.1
intron # 13
splice site 5'
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|86827321|gb|CI270968.1|CI270968
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|88236936|gb|CI234787.1|CI234787
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|27548290|gb|CA766362.2|CA766362
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86482102|gb|CI124735.1|CI124735
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|87037946|gb|CI192568.1|CI192568
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86481113|gb|CI123746.1|CI123746
EST:     ACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: ACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86437635|gb|CI119357.1|CI119357
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|87035950|gb|CI190572.1|CI190572
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTATCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|58674115|gb|CK062801.1|CK062801
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|87038360|gb|CI192982.1|CI192982
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86478214|gb|CI120847.1|CI120847
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|3766575|gb|AU030685.1|AU030685
EST:     CAGCAAGTTCCAAACATGTCTGAGCANTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86477959|gb|CI120592.1|CI120592
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|88834377|gb|CI077660.1|CI077660
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86513692|gb|CI156325.1|CI156325
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86436986|gb|CI118708.1|CI118708
EST:     CAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCGAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86855869|gb|CI271088.1|CI271088
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86437244|gb|CI118966.1|CI118966
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86482048|gb|CI124681.1|CI124681
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCTACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86481992|gb|CI124625.1|CI124625
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86436745|gb|CI118467.1|CI118467
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|29674781|gb|CB671056.1|CB671056
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|87023322|gb|CI272150.1|CI272150
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|87016249|gb|CI271660.1|CI271660
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|88966337|gb|CI119472.1|CI119472
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86481741|gb|CI124374.1|CI124374
EST:     ATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: ATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86478599|gb|CI121232.1|CI121232
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86497710|gb|CI140343.1|CI140343
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|87038839|gb|CI193461.1|CI193461
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86597722|gb|CI274713.1|CI274713
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|87016434|gb|CI273644.1|CI273644
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|86478037|gb|CI120670.1|CI120670
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|87031803|gb|CI272504.1|CI272504
EST:     CATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
EST: gi|87021407|gb|CI274014.1|CI274014
EST:     CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAAT                         GCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC
genomic: CAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGC

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), 73 (downstream exon)
Score: 26

ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgac ... ggcattacagGCAACAAGGAGGTTTGGGTTCCCTCAACATGGGCTTTGATCAACAAGCTGCTCCCAGGTACCCCCAGCCAAGCACCCCACCTTCCTATGGCTCTGTTGGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCATTACATGATGCAGCAAGTTCCAAACATGTCTGAGCAGTTACCTAATACCATGCTTCCAATgtgagttgactgctgtatttagtgtatctcctaagttgaaagtgtagtgaagaactttttagcatttttttaaagatactttttgctcgtgttgattttt

- - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - -  GAGCAG