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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatagatccagtggcatctcaatattgtagatccttttggcaagtaaaaccaatgtctattaagacccttatactgttattgggatttttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAG

Basic information

species Oryza sativa
transcript LOC_Os01g18630.1
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|38477201|gb|CF961334.1|CF961334
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAACAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGG
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGG
EST: gi|29645987|gb|CB650994.1|CB650994
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
EST: gi|300216028|gb|HO088654.1|HO088654
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
EST: gi|117226899|gb|CT848683.1|CT848683
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
EST: gi|29631102|gb|CB636111.1|CB636111
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
EST: gi|29639114|gb|CB644123.1|CB644123
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
EST: gi|33655849|gb|CF278463.1|CF278463
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
EST: gi|29643123|gb|CB648130.1|CB648130
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
EST: gi|29662753|gb|CB659028.1|CB659028
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
EST: gi|29665539|gb|CB661814.1|CB661814
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
EST: gi|33664969|gb|CF295936.1|CF295936
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
EST: gi|29664681|gb|CB660956.1|CB660956
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
EST: gi|300215808|gb|HO088434.1|HO088434
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
EST: gi|88304198|gb|CI599886.1|CI599886
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
EST: gi|218504625|gb|FG968741.1|FG968741
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
EST: gi|38471583|gb|CF955714.1|CF955714
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
EST: gi|33654015|gb|CF276629.1|CF276629
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGGTCTGGATCAATTGCTGGTTTCTTC
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGG-TCTGGATCAATTGCTGGTTTCTTC
EST: gi|29635435|gb|CB640444.1|CB640444
EST:     CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATG                         GAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA
genomic: CTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCA

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: 70 (upstream exon), 69 (downstream exon)
Score: 29

ATAGCATGCTACTTACACCACAGGTACAAGTCAAAAGGGTCGAGCAGTTACAAAAAGAATGgtatgataga ... ttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaaaccaatgtctattaagacccttatactgttattgggatttttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAG
                                          tttttattttc  CT-rich tract
                                         atttttattttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatagatccagtggcatctcaatattgtagatccttttggcaagtaaaaccaatgtctattaagacccttatactgttattgggatttttattttcagGAGAATCTTGCAGCATTTCCTATGGGTCTGGATCAATTGCTGGTTTCTTCAGTGAGGATAGCGTGCTAGTTGGGGATCTTGCTGTGAAAAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT