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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACGGACAGCATCTACATGGAGGTAGAGCACAGGCGACTCTCCTTCATCAAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagacgcatctctgaaagtattctgaacaccgtcttgatgagcagcatgacaaacaacattcttggtggtctttgcag

Basic information

species Oryza sativa
transcript LOC_Os09g35890.1
intron # 13
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|87015156|gb|CI273554.1|CI273554
EST:     AAG-ACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|58684786|gb|CK073473.1|CK073473
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|58682201|gb|CK070888.1|CK070888
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|88993328|gb|CI257756.1|CI257756
EST:     AGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AGAACTCCCTCATCGCAGACGGCGAGCTCCACGC-TACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|86847299|gb|CI285313.1|CI285313
EST:     AAGA-CTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|27548109|gb|CA766211.2|CA766211
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|58675998|gb|CK064685.1|CK064685
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|86436751|gb|CI118473.1|CI118473
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|86477621|gb|CI120254.1|CI120254
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|87013981|gb|CI271372.1|CI271372
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|87017936|gb|CI273958.1|CI273958
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|58677341|gb|CK066028.1|CK066028
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|88983175|gb|CI020739.1|CI020739
EST:     CCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: CCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|89165308|gb|CI102398.1|CI102398
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|86477956|gb|CI120589.1|CI120589
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|58674533|gb|CK063220.1|CK063220
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|86521092|gb|CI161298.1|CI161298
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|86479724|gb|CI122357.1|CI122357
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|58670415|gb|CK059101.1|CK059101
EST:     AACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|86481255|gb|CI123888.1|CI123888
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|86437503|gb|CI119225.1|CI119225
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|58686038|gb|CK074725.1|CK074725
EST:     CAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: CAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|86478074|gb|CI120707.1|CI120707
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|58686354|gb|CK075041.1|CK075041
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|40724701|gb|CK431278.1|CK431278
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|89165292|gb|CI102382.1|CI102382
EST:     AACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|86477263|gb|CI119896.1|CI119896
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATTTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|86437740|gb|CI119660.1|CI119660
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|86479318|gb|CI121951.1|CI121951
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|58680500|gb|CK069187.1|CK069187
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|58677903|gb|CK066590.1|CK066590
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|58604679|gb|CK015207.1|CK015207
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|86593018|gb|CI270575.1|CI270575
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|86480701|gb|CI123334.1|CI123334
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|87021097|gb|CI271904.1|CI271904
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|58675717|gb|CK064404.1|CK064404
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|86480003|gb|CI122636.1|CI122636
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
EST: gi|58678855|gb|CK067542.1|CK067542
EST:     AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAG                         CTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG
genomic: AAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAG

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), 71 (downstream exon)
Score: 19

AGACGGACAGCATCTACATGGAGGTAGAGCACAGGCGACTCTCCTTCATCAAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagac ... gtctttgcagCTTGAGGAATCTTCGGCATGAGAGGGACATGCTGTACAGGCAGATGGTGAGGAAGCTGCACCTGGCCGAGAAGGAGAGGCTGTACGGCAAGTGGGGGATC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACGGACAGCATCTACATGGAGGTAGAGCACAGGCGACTCTCCTTCATCAAGAACTCCCTCATCGCAGACGGCGAGCTCCACGCTACCACCGCATCAAGgttcagagacgcatctctgaaagtattctgaacaccgtcttgatgagcagcatgacaaacaacattcttggtggtctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC