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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtcacattttcgcaattacccaaacacagtagacaacttaaaatgctaaatccaaagctctgaagttgattaattactgtcctttttttattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGACACCGACATCTCGTCCGGGAAGATCTCCTTGAGAAGCTTG

Basic information

species Oryza sativa
transcript LOC_Os02g33110.3
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|58587777|gb|CF986085.1|CF986085
EST:     GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAA                         GTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
genomic: GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
EST: gi|88252292|gb|CI350720.1|CI350720
EST:     TGCACCGACCCTACCAA                         GTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGGTCG
genomic: TGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTC-GTCG
EST: gi|87027005|gb|CI259658.1|CI259658
EST:     CGTCGTCCTCATGTGCACCGACCCTACCAA                         GTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
genomic: CGTCGTCCTCATGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
EST: gi|29660430|gb|CB656705.1|CB656705
EST:     GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAA                         GTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
genomic: GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
EST: gi|4714303|gb|AU058270.1|AU058270
EST:     GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAA                         GTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
genomic: GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
EST: gi|29660456|gb|CB656731.1|CB656731
EST:     GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAA                         GTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
genomic: GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
EST: gi|29660422|gb|CB656697.1|CB656697
EST:     GCCGGGCACGGCGCCAAGCCCGTCGTCTTCATGTGCACCGACCCTACCAA                         GTCTTCTGTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
genomic: GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
EST: gi|88996390|gb|CI259894.1|CI259894
EST:     GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAA                         GTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
genomic: GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
EST: gi|29660484|gb|CB656759.1|CB656759
EST:     GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAA                         GTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
genomic: GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
EST: gi|58590379|gb|CF988687.1|CF988687
EST:     GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAA                         GTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
genomic: GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
EST: gi|29660424|gb|CB656699.1|CB656699
EST:     GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAA                         GTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
genomic: GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
EST: gi|29674131|gb|CB670406.1|CB670406
EST:     GCCGGGCACGGCGCCAAGCCCGTCGTCTTCATGTGCACCGACCCTACCAA                         GTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
genomic: GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
EST: gi|38477539|gb|CF961672.1|CF961672
EST:     TGTGCACCGA-CCTA-CAA                         GTCTTCTCTTAGCCCGGATCTCTACAAGCCAAGC-TTGGCCGGGTTCGTCG
genomic: TGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAA-CTTTTGCCGGGTTCGTCG
EST: gi|87039999|gb|CI194621.1|CI194621
EST:     CCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAA                         GTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
genomic: GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
EST: gi|29660482|gb|CB656757.1|CB656757
EST:     GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAA                         GTCTTCTTTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTAGTCGA
genomic: GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
EST: gi|86500033|gb|CI142666.1|CI142666
EST:     GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAA                         GTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
genomic: GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
EST: gi|29669164|gb|CB665439.1|CB665439
EST:     GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAA                         GTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA
genomic: GCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGA

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: 74 (upstream exon), 73 (downstream exon)
Score: 41

CCGCCGGCCTGGAGGAGAAAACCGCCGTCTTCTTCCGCGTCTTCAAGCCGGCCGGGCACGGCGCCAAGCCCGTCGTCCTCATGTGCACCGACCCTACCAAgtacgatacc ... tattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGACACCGACATCTCGTCCGGGAAGATCTCCTTGAGAAGCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctaaatccaaagctctgaagttgattaattactgtcctttttttattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGACACCGACATCTCGTCCGGGAAGATCTCCTTGAGAAGCTTG
                              ttactgtccttttttt  CT-rich tract
                   aagttgattaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtcacattttcgcaattacccaaacacagtagacaacttaaaatgctaaatccaaagctctgaagttgattaattactgtcctttttttattgagcagGTCTTCTCTTAGCCCGGATCTCTACAAGCCAACTTTTGCCGGGTTCGTCGACACCGACATCTCGTCCGGGAAGATCTCCTTGAGAAGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC