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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttctcccaagaagcacaatatcattgatgtagaaatttgcagtttaaaaacagatatcgtatgatctaactttggcacatatgactgtttatc...

Basic information

species Oryza sativa
transcript LOC_Os02g02560.1
intron # 19
splice site 5'
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|88250631|gb|CI348861.1|CI348861
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|86835725|gb|CI348182.1|CI348182
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|86836204|gb|CI346206.1|CI346206
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|87032112|gb|CI362192.1|CI362192
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|86601109|gb|CI356866.1|CI356866
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGTACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|86595013|gb|CI258267.1|CI258267
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGCGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|7332555|gb|AU085901.1|AU085901
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|88258425|gb|CI361011.1|CI361011
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|86839753|gb|CI343676.1|CI343676
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|88261397|gb|CI364973.1|CI364973
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|88261483|gb|CI365059.1|CI365059
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCACTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATCCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|86835715|gb|CI348172.1|CI348172
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|88260254|gb|CI362547.1|CI362547
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|86479595|gb|CI122228.1|CI122228
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|88261093|gb|CI364669.1|CI364669
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|88256960|gb|CI359348.1|CI359348
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|66947245|gb|AU312089.1|AU312089
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|86859745|gb|CI345407.1|CI345407
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|86834286|gb|CI344046.1|CI344046
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|88252508|gb|CI350936.1|CI350936
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|86598561|gb|CI355178.1|CI355178
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|66922584|gb|CX109432.1|CX109432
EST:     ACCTGGTGTCAAACTGGAAATCCCCAGATGGAGCAGTGATCGAGAACCAG                         GATTTCAATGGCCCCGAGGACCTTTGAAGC-AAAGGGATGCAGAGTTCACC
genomic: ACCTGGTGTCAAACTGGAAATCCC-AGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGA-GCGAAAGG-ATGCAGAGTTCACA
EST: gi|86841180|gb|CI342925.1|CI342925
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|88994067|gb|CI116031.1|CI116031
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|86823815|gb|CI258831.1|CI258831
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
EST: gi|88254412|gb|CI353236.1|CI353236
EST:     AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG                         GATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA
genomic: AACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAA

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: 33 (upstream exon), 75 (downstream exon)
Score: 5

GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttc ... ctcatttcagGATATCAATGGCCCCGAGGACCTTTGAGCGAAAGGATGCAGAGTTCACAAAGAGAGATCATATCACCATTCCATATAATCAATCAAGCTCCACGACATTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAGgtactttttctcccaagaagcacaatatcattgatgtagaaatttgcagtttaaaaacagatatcgtatgatctaactttggcacatatgactgtttatc

- - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaca