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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcacgcatgtttcttttctgacccgtcgttatcttgtatggtctggtatgcaagtggttcatttctagcataccttacatggtaatgccctctgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACACCAAGGGTCGCTTCCGCCTTCAGTCCGTCAAGGATGAGGATGCCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g25610.1
intron # 3
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|87024077|gb|CI291730.1|CI291730
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTC
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTC
EST: gi|88571365|gb|CI662738.1|CI662738
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGAC
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGAC
EST: gi|87007839|gb|CI287683.1|CI287683
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATG
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATG
EST: gi|88358658|gb|CI618746.1|CI618746
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|117249752|gb|CT863374.1|CT863374
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|88423077|gb|CI613378.1|CI613378
EST:     GGTTGATGGGAAGGTCAGGAGTGACAAGACCTACC-TGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|87035387|gb|CI190009.1|CI190009
EST:     TGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: TGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|33661683|gb|CF292650.1|CF292650
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|87035382|gb|CI190004.1|CI190004
EST:     ACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: ACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|33675492|gb|CF303731.1|CF303731
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|218492817|gb|FG968356.1|FG968356
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|33677983|gb|CF306222.1|CF306222
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|58682645|gb|CK071332.1|CK071332
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATCTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|86906924|gb|CI291271.1|CI291271
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|88725669|gb|CI748928.1|CI748928
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTC
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTC
EST: gi|88431411|gb|CI576941.1|CI576941
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|58686532|gb|CK075219.1|CK075219
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATG
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATG
EST: gi|88424643|gb|CI606442.1|CI606442
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|218494994|gb|FG969750.1|FG969750
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|33829204|gb|CF340424.1|CF340424
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTT-CATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|88723386|gb|CI746896.1|CI746896
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGA
EST: gi|58592361|gb|CF990669.1|CF990669
EST:     TACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: TACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|218504837|gb|FG949405.1|FG949405
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCCTGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|88325817|gb|CI649654.1|CI649654
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAAC
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAAC
EST: gi|88358593|gb|CI617679.1|CI617679
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGAGTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|86907280|gb|CI292843.1|CI292843
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|218497016|gb|FG965105.1|FG965105
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|88365015|gb|CI616434.1|CI616434
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGC
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGC
EST: gi|88387470|gb|CI582988.1|CI582988
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTT-CATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATG
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATG
EST: gi|218478245|gb|FG957059.1|FG957059
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
EST: gi|58675811|gb|CK064498.1|CK064498
EST:     GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGG                         ATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA
genomic: GGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACA

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: 63 (upstream exon), 71 (downstream exon)
Score: 54

GCGCTGACATACCGTGAGGTTATCTCTATCCTGATGCAGCGGCATGTCTTGGTTGATGGGAAGGTCAGGACTGACAAGACCTACCCTGCTGGTTTCATGGgtatgcacgc ... tgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACACCAAGGGTCGCTTCCGCCTTCAGTCCGTCAAGGATGAGGATGCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcaagtggttcatttctagcataccttacatggtaatgccctctgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACACCAAGGGTCGCTTCCGCCTTCAGTCCGTCAAGGATGAGGATGCCAAG
                        accttac  putative branch site (score: 54)
                                        ccctctgttt  putative PPT
          ttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcacgcatgtttcttttctgacccgtcgttatcttgtatggtctggtatgcaagtggttcatttctagcataccttacatggtaatgccctctgtttggcagATGTGATTTCCATTCCAAAGACTGGTGAGAACTACAGGCTTCTCTATGACACCAAGGGTCGCTTCCGCCTTCAGTCCGTCAAGGATGAGGATGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG