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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaataaaaatatggctctggctatagcatctacttgtactggttagctggatgaggatgaattccactgatgcattttggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAATAGATTATGTAATTAAGCAAG

Basic information

species Oryza sativa
transcript LOC_Os03g49610.1
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|58664486|gb|CK053172.1|CK053172
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58667486|gb|CK056172.1|CK056172
EST:     AATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: AATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGG-ATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58670861|gb|CK059547.1|CK059547
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58672531|gb|CK061217.1|CK061217
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58673207|gb|CK061893.1|CK061893
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58663907|gb|CK052593.1|CK052593
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58666291|gb|CK054977.1|CK054977
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58667025|gb|CK055711.1|CK055711
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGA
EST: gi|58662636|gb|CK051322.1|CK051322
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58672509|gb|CK061195.1|CK061195
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|117229561|gb|CT859875.1|CT859875
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58669370|gb|CK058056.1|CK058056
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58669614|gb|CK058300.1|CK058300
EST:     GAATTTCGATGCATATCGGTTTACAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAAATAATCTA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAA-TAATCTA
EST: gi|58652616|gb|CK041296.1|CK041296
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58663559|gb|CK052245.1|CK052245
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58678605|gb|CK067292.1|CK067292
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58654026|gb|CK042706.1|CK042706
EST:     GAATTTCGATGCATATCGG-TGTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58665258|gb|CK053944.1|CK053944
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58678530|gb|CK067217.1|CK067217
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGA-TTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58653039|gb|CK041719.1|CK041719
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58656093|gb|CK044773.1|CK044773
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAA
EST: gi|58670581|gb|CK059267.1|CK059267
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAACAGTTAACACCGGAAGGTGTGGCATATTACA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACAC-GGAAGGTGTGGCATATTACA
EST: gi|58670130|gb|CK058816.1|CK058816
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58612072|gb|CK039784.1|CK039784
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
EST: gi|58669526|gb|CK058212.1|CK058212
EST:     GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG                         ATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA
genomic: GAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAA

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: 32 (upstream exon), 62 (downstream exon)
Score: 33

GAAGATGTTGATCTCTTGAAAAGCCTGAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTGgtaaataaaa ... ggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAATAGATTATGTAATTAAGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtactggttagctggatgaggatgaattccactgatgcattttggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAATAGATTATGTAATTAAGCAAG
                               cactgat  putative branch site (score: 33)
                                        attttggttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaataaaaatatggctctggctatagcatctacttgtactggttagctggatgaggatgaattccactgatgcattttggttatttagATGGAGAGGGAAAAGTTAACACGGAAGGTGTGGCATATTACAATAATCTAATAGATTATGTAATTAAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG