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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaatttccattcaacagttctctatattctcaatatcaatactagtttcatggctcatgagcatatggctgtacaatggctggccggcagcaca...

Basic information

species Oryza sativa
transcript LOC_Os01g72650.1
intron # 3
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|88315637|gb|CI615509.1|CI615509
EST:     GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAG                         ATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
genomic: GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
EST: gi|58662600|gb|CK051286.1|CK051286
EST:     GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAG                         ATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
genomic: GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
EST: gi|88305463|gb|CI630625.1|CI630625
EST:     GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAG                         ATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
genomic: GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
EST: gi|88337451|gb|CI630748.1|CI630748
EST:     GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAG                         ATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
genomic: GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
EST: gi|88315936|gb|CI618812.1|CI618812
EST:     GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAG                         ATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
genomic: GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
EST: gi|88347090|gb|CI631170.1|CI631170
EST:     GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAG                         ATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
genomic: GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
EST: gi|88582438|gb|CI699851.1|CI699851
EST:     GATAACAAACAAGGCAGCTGGAAAGGCTATATTCATCAAAATGGACCCAG                         ATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTC
genomic: GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTC
EST: gi|88372401|gb|CI619731.1|CI619731
EST:     GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAG                         ATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
genomic: GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
EST: gi|88345614|gb|CI629875.1|CI629875
EST:     ANTA-CAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAG                         ATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
genomic: A-TAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
EST: gi|88353355|gb|CI631540.1|CI631540
EST:     GATAACAAACAAGGCAGCTGCCAAGGCTATATTCATCAAAATGGACCCAG                         ATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGCTAAAA
genomic: GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
EST: gi|88337722|gb|CI632224.1|CI632224
EST:     GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAG                         ATCAAGTGGAGACTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
genomic: GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
EST: gi|88353396|gb|CI631581.1|CI631581
EST:     ATAACAAACAAGGGAGCTGCAAAGGCTATATTCATCAAAATGGACCCCAG                         ATCAAGTGGAGATTCCCTTTAACGTGCTTCAGGAGAGAGTCCCTGGTAAA
genomic: ATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCC-AGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAA
EST: gi|88587934|gb|CI705716.1|CI705716
EST:     GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAC                         ATCAAGTGGAGATCCCCTTNAAAGTGCTTCAGGAGAGAGTCCCTGCTAAAA
genomic: GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
EST: gi|66923971|gb|CX110819.1|CX110819
EST:     GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAG                         ATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
genomic: GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
EST: gi|88305629|gb|CI631996.1|CI631996
EST:     GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAG                         ATCAAGTGGAGATTCCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAA
genomic: GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCC-TTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAA
EST: gi|88348771|gb|CI631465.1|CI631465
EST:     GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAG                         ATTAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAC
genomic: GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA
EST: gi|88353381|gb|CI631566.1|CI631566
EST:     GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAG                         ATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGCTAAAA
genomic: GATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAA

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: 36 (upstream exon), 40 (downstream exon)
Score: 2

TAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaat ... tttgctctagATCAAGTGGAGATTCCCTTTAAAGTGCTTCAGGAGAGAGTCCCTGGTAAAAAGAAGTATTCCTTAAGGGTTATCAAACCTTCGTCCTCAAAGAAGATATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGCTCCTTGATATTCTGATAACAAACAAGGCAGCTGCAAAGGCTATATTCATCAAAATGGACCCAGgtatgtaaatttccattcaacagttctctatattctcaatatcaatactagtttcatggctcatgagcatatggctgtacaatggctggccggcagcaca

- - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cggcagc