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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcttatcatcttatcaatagaagatacagtaagatttcaccgaggctttcatcagttgcaaattgattaattagtggcacgcgattaactaaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCGGCGTCGTACGAGAAGGCGGTGGCGTGGAAGGTGGTCGACGGCGACGGCG

Basic information

species Oryza sativa
transcript LOC_Os01g10320.1
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|87038823|gb|CI193445.1|CI193445
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|87040163|gb|CI193372.1|CI193372
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|87041427|gb|CI196049.1|CI196049
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|88233153|gb|CI233002.1|CI233002
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|87037181|gb|CI191803.1|CI191803
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|12623143|gb|AU173356.1|AU173356
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|88233061|gb|CI232910.1|CI232910
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|88198498|gb|CI198348.1|CI198348
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGNCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|87039351|gb|CI193973.1|CI193973
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|88197992|gb|CI197842.1|CI197842
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|86432244|gb|CI085855.1|CI085855
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|86258487|gb|CI064840.1|CI064840
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|87038791|gb|CI193413.1|CI193413
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|88198299|gb|CI198149.1|CI198149
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|88229033|gb|CI228909.1|CI228909
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|88233255|gb|CI233104.1|CI233104
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|87032839|gb|CI187463.1|CI187463
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|88197634|gb|CI197484.1|CI197484
EST:     TCCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: TC-AAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|88197643|gb|CI197493.1|CI197493
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|87040405|gb|CI195027.1|CI195027
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|88233135|gb|CI232984.1|CI232984
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
EST: gi|87038456|gb|CI193078.1|CI193078
EST:     ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAG                         GGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG
genomic: ATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCG

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: 38 (upstream exon), 38 (downstream exon)
Score: 1

AACAACTCTGGTGGCGCTCCAAGACATGACGCTGGAGAAAGTTTTCGACGATCAAGGGAGGAAGAACCTGTGCACAGAGCTCCCCAACATCATGGAGCAGgtataatcat ... taaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCGGCGTCGTACGAGAAGGCGGTGGCGTGGAAGGTGGTCGACGGCGACGGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttcatcagttgcaaattgattaattagtggcacgcgattaactaaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCGGCGTCGTACGAGAAGGCGGTGGCGTGGAAGGTGGTCGACGGCGACGGCG
                                          aactaaa  putative branch site (score: 1)
               aaattgattaattagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcttatcatcttatcaatagaagatacagtaagatttcaccgaggctttcatcagttgcaaattgattaattagtggcacgcgattaactaaattgcagGGGATGGCGTGCATGGAGGGAGGGGTGTGCGTGTCGAGCGTTGGGAGGGCGGCGTCGTACGAGAAGGCGGTGGCGTGGAAGGTGGTCGACGGCGACGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - -caatagaa
- - - - - - - - - - - - - - - - - - ttcaccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - agttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcacgc