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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggtgaaaagtaacataacatgtagtggatcttgtctattatgcgcaacacacgacaccctttcttcatttgatgttccaagctgactgactttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCATGGTGTGTGGGACTTGAGGAGGGATGGACGAAAGCGGATCCTCGGGGAA

Basic information

species Oryza sativa
transcript LOC_Os10g27230.2
intron # 11
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|89195904|gb|CI007323.1|CI007323
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88282956|gb|CI404204.1|CI404204
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|86251336|gb|CI055469.1|CI055469
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88510641|gb|CI438147.1|CI438147
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88413586|gb|CI526148.1|CI526148
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|29613589|gb|CB618602.1|CB618602
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGACGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88836259|gb|CI371364.1|CI371364
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         TTCGCGAATAGATGGTTAACTTCTGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|86877680|gb|CI312913.1|CI312913
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|86537140|gb|CI177346.1|CI177346
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|29627416|gb|CB632427.1|CB632427
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGACGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88447964|gb|CI538967.1|CI538967
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATNCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88255136|gb|CI353960.1|CI353960
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88506490|gb|CI433996.1|CI433996
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88468436|gb|CI514918.1|CI514918
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|89178928|gb|CI391926.1|CI391926
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88983097|gb|CI020661.1|CI020661
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88320509|gb|CI523252.1|CI523252
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|89180086|gb|CI044365.1|CI044365
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88219644|gb|CI219204.1|CI219204
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88374432|gb|CI515916.1|CI515916
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|4716458|gb|AU057574.1|AU057574
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88268411|gb|CI378346.1|CI378346
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|29676248|gb|CB672523.1|CB672523
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|29630215|gb|CB635224.1|CB635224
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGACGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88846729|gb|CI373497.1|CI373497
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|29623249|gb|CB628260.1|CB628260
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGACGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88268979|gb|CI380277.1|CI380277
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88462659|gb|CI517188.1|CI517188
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|88459026|gb|CI514307.1|CI514307
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
EST: gi|89179877|gb|CI044156.1|CI044156
EST:     CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAG                         GTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA
genomic: CTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCA

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: 68 (upstream exon), 65 (downstream exon)
Score: 18

GAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATATAGCACTCTTGGCAGAATTCCGGTGCAAGCCTAGAATCAGACGGTGACACCTTAGgtatgtcata ... ctttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCATGGTGTGTGGGACTTGAGGAGGGATGGACGAAAGCGGATCCTCGGGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacacacgacaccctttcttcatttgatgttccaagctgactgactttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCATGGTGTGTGGGACTTGAGGAGGGATGGACGAAAGCGGATCCTCGGGGAA
                                       gactgac  putative branch site (score: 18)
                                             ctttcttc  CT-rich tract
                   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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cggtgaaaagtaacataacatgtagtggatcttgtctattatgcgcaacacacgacaccctttcttcatttgatgttccaagctgactgactttcttcagGTCGCGAATAGATGGTTAACTTCAGCACCCATGCGGTGGAACATTCTTCCATGGTGTGTGGGACTTGAGGAGGGATGGACGAAAGCGGATCCTCGGGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA