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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATGGAGAGAATCACTCAGCAACTTGGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATGgtaagttgatcaagtttgcacagcattgaccaaagttaagatcgttggcttccttggatgtgaccaatcgccgcgtgtatatatatcag

Basic information

species Oryza sativa
transcript LOC_Os06g10880.1
intron # 4
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|86491535|gb|CI134168.1|CI134168
EST:     GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATG                         CTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
genomic: GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATGgtaagttgat ... tatatatcagCTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
EST: gi|89185524|gb|CI051852.1|CI051852
EST:     GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATG                         CTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
genomic: GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATGgtaagttgat ... tatatatcagCTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
EST: gi|86493779|gb|CI136412.1|CI136412
EST:     GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATG                         CTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
genomic: GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATGgtaagttgat ... tatatatcagCTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
EST: gi|29656994|gb|CB653269.1|CB653269
EST:     GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATG                         CTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
genomic: GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATGgtaagttgat ... tatatatcagCTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
EST: gi|88221385|gb|CI221341.1|CI221341
EST:     TGCCTCCGACGAACACTGACTGGTCCATG                         CTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
genomic: TGCCTCCGACGAACACTGACTGGTCCATGgtaagttgat ... tatatatcagCTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
EST: gi|88833398|gb|CI076879.1|CI076879
EST:     GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATG                         CTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
genomic: GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATGgtaagttgat ... tatatatcagCTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
EST: gi|88446793|gb|CI526626.1|CI526626
EST:     CGAACACTGACTGGTCCATG                         CTGAAGCCAGAGTCTCCGGTTTCNCCNTGGCGCTCAGCTTCAGAGTTGCTT
genomic: CGAACACTGACTGGTCCATGgtaagttgat ... tatatatcagCTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
EST: gi|86414073|gb|CI068280.1|CI068280
EST:     GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATG                         CTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
genomic: GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATGgtaagttgat ... tatatatcagCTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
EST: gi|88520057|gb|CI447711.1|CI447711
EST:     GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATG                         CTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
genomic: GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATGgtaagttgat ... tatatatcagCTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
EST: gi|86492892|gb|CI135525.1|CI135525
EST:     GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATG                         CTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
genomic: GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATGgtaagttgat ... tatatatcagCTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
EST: gi|87028268|gb|CI111962.1|CI111962
EST:     GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATG                         CTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT
genomic: GGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATGgtaagttgat ... tatatatcagCTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTT

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: 59 (upstream exon), 74 (downstream exon)
Score: 13

GTCATGGAGAGAATCACTCAGCAACTTGGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATGgtaagttgat ... tatatatcagCTGAAGCCAGAGTCTCCGGTTTCGCCGTGGCGCTCAGCTTCAGAGTTGCTTCTCTCCTTGTTGGTGAATGGTGATGGCTCAGTCTCTTGGACGGTCGAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATGGAGAGAATCACTCAGCAACTTGGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATGgtaagttgatcaagtttgcacagcattgaccaaagttaagatcgttggcttccttggatgtgaccaatcgccgcgtgtatatatatcag

- - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - -  AAGAGA