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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgccttcgttgtttcaaagcttagttcagttctgcattgcttctgtgatggaaatgtttatcaacttactatgatgtcttcgcaactgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCAGGACAACCGTCACAAACCCCAAGGCCAAAGCTTTGAGAGGTGCAGAAGA

Basic information

species Oryza sativa
transcript LOC_Os04g47120.1
intron # 16
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|88974436|gb|CI021977.1|CI021977
EST:     CGGTGGGCGGGGTTTTGTTACACGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGGCA
genomic: CGGTGGGCGGGGTTTTGTTACA-GGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|86430173|gb|CI082596.1|CI082596
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|87005717|gb|CI316136.1|CI316136
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88254772|gb|CI353596.1|CI353596
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|86863469|gb|CI345210.1|CI345210
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|89177316|gb|CI250765.1|CI250765
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|58609050|gb|CK037083.1|CK037083
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGG-GGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88255678|gb|CI354502.1|CI354502
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88506400|gb|CI433906.1|CI433906
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88455844|gb|CI526660.1|CI526660
EST:     GGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: GGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|86860786|gb|CI325017.1|CI325017
EST:     ACGGTGGTCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|86844554|gb|CI338574.1|CI338574
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88829709|gb|CI074579.1|CI074579
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88267559|gb|CI379494.1|CI379494
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88250752|gb|CI348982.1|CI348982
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88218896|gb|CI216894.1|CI216894
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|87026186|gb|CI278310.1|CI278310
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|86429359|gb|CI076040.1|CI076040
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|86878942|gb|CI315384.1|CI315384
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|29670926|gb|CB667201.1|CB667201
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88290282|gb|CI550504.1|CI550504
EST:     GGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: GGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88321078|gb|CI530430.1|CI530430
EST:     TGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: TGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|86434548|gb|CI105781.1|CI105781
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88843985|gb|CI008566.1|CI008566
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|86487750|gb|CI130383.1|CI130383
EST:     ACGGTGGGCGGGTTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|33681707|gb|CF309946.1|CF309946
EST:     CGGTGGGCGGGGGTTTTGTCACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTANGAGGGCGAAGACGCCA
genomic: CGGTGGGCGGGG-TTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88457318|gb|CI534316.1|CI534316
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88971423|gb|CI017737.1|CI017737
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|86426203|gb|CI071300.1|CI071300
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88489955|gb|CI427227.1|CI427227
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88469972|gb|CI407243.1|CI407243
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88489413|gb|CI426685.1|CI426685
EST:     C-GTGGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATNTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: CGGT-GGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88254212|gb|CI352838.1|CI352838
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|22304837|gb|BQ906059.1|BQ906059
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|86490744|gb|CI133377.1|CI133377
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|88959770|gb|CI002380.1|CI002380
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
EST: gi|86844461|gb|CI337736.1|CI337736
EST:     ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG                         CTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA
genomic: ACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCA

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: 49 (upstream exon), 53 (downstream exon)
Score: 20

ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAGgtatatgcct ... actgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCAGGACAACCGTCACAAACCCCAAGGCCAAAGCTTTGAGAGGTGCAGAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctgtgatggaaatgtttatcaacttactatgatgtcttcgcaactgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCAGGACAACCGTCACAAACCCCAAGGCCAAAGCTTTGAGAGGTGCAGAAGA
                       aacttac  putative branch site (score: 20)
                                              ctgcttt  putative PPT
            aaatgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgccttcgttgtttcaaagcttagttcagttctgcattgcttctgtgatggaaatgtttatcaacttactatgatgtcttcgcaactgctttagCTCGTCATGTCGTTGACCCAAGAGGCGCTGATTAGGAGGGCGAAGACGCCAGGACAACCGTCACAAACCCCAAGGCCAAAGCTTTGAGAGGTGCAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG