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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgccatttattcatacttatgggattgtaaaattcatcaatgctctgtttgataagtatactggaagattttctaatgctgtcttctactttttttcagGCCCGAATCATATGATGATGGAG

Basic information

species Oryza sativa
transcript LOC_Os09g26880.3
intron # 4
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|33676797|gb|CF305036.1|CF305036
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|29668655|gb|CB664930.1|CB664930
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|29617477|gb|CB622489.1|CB622489
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|29668604|gb|CB664879.1|CB664879
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|29656047|gb|CB652322.1|CB652322
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|33797257|gb|CF324491.1|CF324491
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|29656045|gb|CB652320.1|CB652320
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|29668613|gb|CB664888.1|CB664888
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|29638871|gb|CB643880.1|CB643880
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|33683878|gb|CF312117.1|CF312117
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|29665768|gb|CB662043.1|CB662043
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|33681819|gb|CF310058.1|CF310058
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGANTGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGA-TGATGGAG
EST: gi|29673829|gb|CB670104.1|CB670104
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|29655872|gb|CB652147.1|CB652147
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|29661446|gb|CB657721.1|CB657721
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|33675985|gb|CF304224.1|CF304224
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|29674834|gb|CB671109.1|CB671109
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|59930146|gb|AB178688.1|AB178688
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCAAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|58689444|gb|CK078131.1|CK078131
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCAAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|29673252|gb|CB669527.1|CB669527
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|29628521|gb|CB633532.1|CB633532
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCAAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|29668647|gb|CB664922.1|CB664922
EST:     TGCTGTGGGCCTACGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|29677488|gb|CB673763.1|CB673763
EST:     TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG
EST: gi|29668563|gb|CB664838.1|CB664838
EST:     TGCTGTGGGCCTAAGTCTCCAGCTAAATGGGTCCATCATACCATCTGAAC                         GCCCGAATCATATGATGATGGAG
genomic: TGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG

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: 73 (upstream exon), 73 (downstream exon)
Score: 90

GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAACgtaagcccat ... tttttttcagGCCCGAATCATATGATGATGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttgataagtatactggaagattttctaatgctgtcttctactttttttcagGCCCGAATCATATGATGATGGAG
                          ttctaat  putative branch site (score: 90)
                                tgctgtcttctacttt  CT-rich tract
                       attttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgccatttattcatacttatgggattgtaaaattcatcaatgctctgtttgataagtatactggaagattttctaatgctgtcttctactttttttcagGCCCGAATCATATGATGATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
-tgccatt
- - - - - - - - - - - - - - - - - - -tcaatgc
- - - - - - - - - - - - - - - - - - - - - - -ctgtttg