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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgctctcctgatagtttgcacaagtatgttgattgttctcatatcattcaaacataactgttcttaacttcttttctcttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTATTACTGACGAAGAGGGCATAATGCAACTCCTG

Basic information

species Oryza sativa
transcript LOC_Os12g07190.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G126656_T01 (Zea mays), 3'ss of exon 11
gtaattgctctcctgatagtttgcacaagtatgttgattgttctcatatcattcaaacataactg-ttcttaacttcttttctc-ttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTATTACTGACGAAGAGGGCATAATGCAACTCCTG
||| ||  |      ||||||| |      ||||    | |  |   | |  ||||  ||||| | || || | || |    || || |||||||||||||||||||  ||||||| | ||||||| ||| |||||||||||||||| |||| ||| | |      |||||||| ||
gtatttatttgttccatagtttacctgcagatgtaagatatgattgcaac-ctcaattataaccgattgtttatttttcaattcattactgcagGCTCAGAGAGCTTGGACGAGCTTGTGTCTTCTGTAAGACAAAGATTAAGTATTGCTGATGAAAAAGAAGCTGTGCAACTCTTG
















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|58674052|gb|CK062738.1|CK062738
EST:     TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTG                         GCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
genomic: TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTGgtaattgctc ... cttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
EST: gi|29617499|gb|CB622511.1|CB622511
EST:     TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTG                         GCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
genomic: TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTGgtaattgctc ... cttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
EST: gi|29616352|gb|CB621364.1|CB621364
EST:     TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTG                         GCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
genomic: TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTGgtaattgctc ... cttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
EST: gi|29658205|gb|CB654480.1|CB654480
EST:     TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTG                         GCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
genomic: TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTGgtaattgctc ... cttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
EST: gi|29677624|gb|CB673899.1|CB673899
EST:     CAAAAGGGACGCGTGCATAGATTCACTTGTG                         GCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
genomic: CAAAAGGGACGCGTGCATAGATTCACTTGTGgtaattgctc ... cttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
EST: gi|29628515|gb|CB633526.1|CB633526
EST:     TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTG                         GCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
genomic: TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTGgtaattgctc ... cttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
EST: gi|29620737|gb|CB625748.1|CB625748
EST:     TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTG                         GCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
genomic: TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTGgtaattgctc ... cttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
EST: gi|29657212|gb|CB653487.1|CB653487
EST:     GCCTTTAAGCTTCAAGACCAAAAGGGGACGCGTGCATAGATTCACTTGTG                         GCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
genomic: GCCTTTAAGCTTCAAGACCAAAA-GGGACGCGTGCATAGATTCACTTGTGgtaattgctc ... cttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
EST: gi|29683888|gb|CB680163.1|CB680163
EST:     TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTG                         GCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
genomic: TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTGgtaattgctc ... cttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
EST: gi|33799726|gb|CF325729.1|CF325729
EST:     TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTG                         GCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
genomic: TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTGgtaattgctc ... cttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
EST: gi|29658285|gb|CB654560.1|CB654560
EST:     TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTG                         GCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
genomic: TGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTGgtaattgctc ... cttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
EST: gi|86501420|gb|CI144053.1|CI144053
EST:     ATTCACTTGTG                         GCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
genomic: ATTCACTTGTGgtaattgctc ... cttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
EST: gi|66916619|gb|CX103467.1|CX103467
EST:     CAAGA-CAAAAGGGACGCGTGCATAGATTCACTTGTG                         GCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA
genomic: CAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTGgtaattgctc ... cttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTA

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: 68 (upstream exon), 72 (downstream exon)
Score: 24

ACTGGAGATGGAAAGAGTAGCATTTACCCCCCTGTTATTGGAAATTCGTTTGCCTTTAAGCTTCAAGACCAAAAGGGACGCGTGCATAGATTCACTTGTGgtaattgctc ... cttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTATTACTGACGAAGAGGGCATAATGCAACTCCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttctcatatcattcaaacataactgttcttaacttcttttctcttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTATTACTGACGAAGAGGGCATAATGCAACTCCTG
                             tcttaac  putative branch site (score: 24)
                         ctgttcttaacttctt  CT-rich tract
        atatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgctctcctgatagtttgcacaagtatgttgattgttctcatatcattcaaacataactgttcttaacttcttttctcttgctgcagGCTCAGAGAGCTTAAACGAGCTAGCGTCTTCTATAAAACAAAGATTAAGTATTACTGACGAAGAGGGCATAATGCAACTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG