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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacttaaatctgtcgctaaatcgataatatggttttttactatattttggagcttcaagtaccttggtctgctaacaatgaaagaaactcctttgtgcagGTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAG

Basic information

species Oryza sativa
transcript LOC_Os05g43540.1
intron # 7
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|88466361|gb|CI529770.1|CI529770
EST:     GATCCAAAAGATACGTTGTTAATGGAGTTGCAATGTTTCTTACTTGGCTG                         GTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACAT
genomic: GATCCAAAAGATACGTTGTTAATGGAGTTGCAATGTTTCTTACTTGGCTGgtaagaataa ... ctttgtgcagGTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACAT
EST: gi|88839208|gb|CI378132.1|CI378132
EST:     GATCCAAAAGATACGTTGTTAATGGAGTTGCAATGTTTCTTACTTGGCTG                         GTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACAT
genomic: GATCCAAAAGATACGTTGTTAATGGAGTTGCAATGTTTCTTACTTGGCTGgtaagaataa ... ctttgtgcagGTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACAT
EST: gi|88956742|gb|CI009012.1|CI009012
EST:     GTTTCTTACTTGGCTG                         GTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACAT
genomic: GTTTCTTACTTGGCTGgtaagaataa ... ctttgtgcagGTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACAT
EST: gi|33691827|gb|CF320066.1|CF320066
EST:     GATCCAAAAGATACGTTGTTAATGGAGTTGCAATGTTTCTTACTTGGCTG                         GTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACAT
genomic: GATCCAAAAGATACGTTGTTAATGGAGTTGCAATGTTTCTTACTTGGCTGgtaagaataa ... ctttgtgcagGTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACAT
EST: gi|88560412|gb|CI491071.1|CI491071
EST:     TGTTTCTTACTTGGCTG                         GTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACAT
genomic: TGTTTCTTACTTGGCTGgtaagaataa ... ctttgtgcagGTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACAT
EST: gi|88296681|gb|CI537648.1|CI537648
EST:     GATCCAAAAGATACGTTGTTAATGGAGTTGCAATGTTTCTTACTTGGCTG                         GTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACAT
genomic: GATCCAAAAGATACGTTGTTAATGGAGTTGCAATGTTTCTTACTTGGCTGgtaagaataa ... ctttgtgcagGTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACAT
EST: gi|29666719|gb|CB662994.1|CB662994
EST:     GATCCAAAAGATACGTTGTTAATGGAGTTGCAATGTTTCTTACTTGGCTG                         GTTGCAAGGATAATTTTGNTCATGT
genomic: GATCCAAAAGATACGTTGTTAATGGAGTTGCAATGTTTCTTACTTGGCTGgtaagaataa ... ctttgtgcagGTTGCAAGGATAATTTTGTTCATGT
EST: gi|88522122|gb|CI449856.1|CI449856
EST:     TTACTTGGCTG                         GTGGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACAT
genomic: TTACTTGGCTGgtaagaataa ... ctttgtgcagGTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACAT
EST: gi|29666720|gb|CB662995.1|CB662995
EST:     GATCCAAAAGATACGTTGTTAATGGAGTTGCAATGTTTCTTACTTGGCTG                         GTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACAT
genomic: GATCCAAAAGATACGTTGTTAATGGAGTTGCAATGTTTCTTACTTGGCTGgtaagaataa ... ctttgtgcagGTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACAT

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: 72 (upstream exon), 60 (downstream exon)
Score: 17

GTTCCTTGATGTTGCTGGAATGAAAAGATCCAAAAGATACGTTGTTAATGGAGTTGCAATGTTTCTTACTTGGCTGgtaagaataa ... ctttgtgcagGTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggagcttcaagtaccttggtctgctaacaatgaaagaaactcctttgtgcagGTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAG
                        tgctaac  putative branch site (score: 17)
                                          ctcctttgt  putative PPT
                           taacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacttaaatctgtcgctaaatcgataatatggttttttactatattttggagcttcaagtaccttggtctgctaacaatgaaagaaactcctttgtgcagGTTGCAAGGATAATTTTGTTCATGTACTTGTTTTATCAGATCTTTTTACATTATGATCAG

- - - - - tgtcgct
- - - - - - - - - - - - - - - - - - - - - - - -tggagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaaa