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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaaaatcgatcaatcagtcgtgtgtgccacattaagagatgtgtatatgtcgatgtcaaatgacaattgcaattaataactattacaaaccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCGCAACTCACGTGCTAAAGGTTGAGGTGTTGGAGGTTAAGAGCAGGGTGGG

Basic information

species Oryza sativa
transcript LOC_Os12g36850.1
intron # 1
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|88385248|gb|CI630349.1|CI630349
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATACTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|325493041|gb|JG457565.1|JG457565
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|88210972|gb|CI212612.1|CI212612
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|88995988|gb|CI037279.1|CI037279
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|15857263|gb|BI810075.1|BI810075
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCCAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|87025579|gb|CI254625.1|CI254625
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|55439606|gb|CV733113.1|CV733113
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|88350581|gb|CI630025.1|CI630025
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|88345563|gb|CI629824.1|CI629824
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|55433325|gb|CV729736.1|CV729736
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|88327682|gb|CI657720.1|CI657720
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|86594486|gb|CI253385.1|CI253385
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|86499995|gb|CI142628.1|CI142628
EST:     CGAGGGGAATGGCGGCCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACCAAGACCAAAATAGTGGTGTGCGACAGC
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATA-CAAGACCAAAATAGTGGTGTGCGACAGC
EST: gi|55437556|gb|CV732056.1|CV732056
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|55435218|gb|CV730740.1|CV730740
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|88348683|gb|CI631377.1|CI631377
EST:     GAGGGGAATGGCGGGCCGGGCCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: GAGGGGAATGGCGGGCCGGGC-ACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|88327903|gb|CI648302.1|CI648302
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|55436892|gb|CV731625.1|CV731625
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|87019262|gb|CI279772.1|CI279772
EST:     CGAGGGGAATGTCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|88212599|gb|CI212239.1|CI212239
EST:     GCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: GCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|117246698|gb|CT848528.1|CT848528
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|86528322|gb|CI168528.1|CI168528
EST:     GAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: GAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|88765892|gb|CI774982.1|CI774982
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|88351551|gb|CI628771.1|CI628771
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGC
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCC-GCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGC
EST: gi|25799171|gb|CA755132.1|CA755132
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACNAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|88335314|gb|CI650279.1|CI650279
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|55441295|gb|CV733963.1|CV733963
EST:     ACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGGGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: ACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|88385231|gb|CI630332.1|CI630332
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|86901863|gb|CI298510.1|CI298510
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGCAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGC
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGG-AGCGTATACAAGACCAAAATAGTGGTGTGCGACAGC
EST: gi|88345219|gb|CI628473.1|CI628473
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|38480055|gb|CF964144.1|CF964144
EST:     GAGGGGAATGGCGGGCCGGGCACCATCCAGAGTCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: GAGGGGAATGGCGGGCCGGGCACCATCCACA-TCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|88237628|gb|CI237477.1|CI237477
EST:     CATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|88208230|gb|CI208079.1|CI208079
EST:     GGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: GGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|27577882|gb|CB000577.1|CB000577
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
EST: gi|88305754|gb|CI632121.1|CI632121
EST:     CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTG                         CCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG
genomic: CGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCG

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: 50 (upstream exon), 75 (downstream exon)
Score: 28

GTGCACTCCCTGCCCAAGGTCTGCGCCGGATTCATCGACGCCGTCGAGGTCGAGGGGAATGGCGGGCCGGGCACCATCCACATCATGAAGCTTAACCCTGgtaggtcccg ... ccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCGCAACTCACGTGCTAAAGGTTGAGGTGTTGGAGGTTAAGAGCAGGGTGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgtcgatgtcaaatgacaattgcaattaataactattacaaaccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCGCAACTCACGTGCTAAAGGTTGAGGTGTTGGAGGTTAAGAGCAGGGTGGG
                             taataac  putative branch site (score: 28)
                    aattgcaattaataac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatcgatcaatcagtcgtgtgtgccacattaagagatgtgtatatgtcgatgtcaaatgacaattgcaattaataactattacaaaccatatgcagCCGCGGACGCAGGGAGCGTATACAAGACCAAAATAGTGGTGTGCGACAGCGCAACTCACGTGCTAAAGGTTGAGGTGTTGGAGGTTAAGAGCAGGGTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - -tgtgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aattgca