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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgctttattagatttatctatcaaacagacttggtctctgccctttttctgtatttttttggtacaaatgtaacagtggtttgcactgttcatgctcagGACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTAAGCAAAAGAAAAGATTGGTATAAGATCCTTGGCATTTCAAAGACGGCAT

Basic information

species Oryza sativa
transcript LOC_Os02g10180.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10180.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G341404_T01 (Zea mays), 3'ss of exon 8
--atgctttattagatttatctatcaaacagacttggtc---tctgccctttttctgtatttttttggtacaaatgtaacagtggtttgcactgttcatgctcagGACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTAAGCAAAAGAAAAGATTGGTATAAGATCCTTGGCATTTCAAAGACGGCAT
  ||    |     ||  |   ||||   | | ||| |    | ||   ||| | | |  |||| || ||  |   ||||      |  || | || |    ||||||||||| ||||| |||||||| |||||||||||||||||||||||||| |||||||||||||| |||||||| ||||||||  |||||||||| ||||
aaatctaatgaagaatgaactgatcatgaatatttgatggaatatgaagtttatttttggttttctgttagcatgataac-----ctaacatttttaacaaccagGACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTGAGCAAAAGAAAAGACTGGTATAAAATCCTTGGTGTTTCAAAGACAGCAT

upper sequence: LOC_Os02g10180.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G03160.1 (Arabidopsis thaliana), 3'ss of exon 7
atgctttattagatttatctatcaaacagacttggtctctgccctttttctgtatttttttggtacaaatgtaacagtggtttgcactgttcatgctcagGACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTAAGCAAAAGAAAAGATTGGTATAAGATCCTTGGCATTTCAAAGACGGCAT
    ||  | | |  |   | |  |       || | |||    | |  ||    | ||  |   ||| |  ||||    | |  | |||        ||||||||| ||| |  ||| ||||    | ||| || ||    || ||| | |||||| ||||||||||||||||||| ||||| ||||| |  || || |
---gttggtgaaagattagtgttcagtgtttctgatatctaaaatgtagcttagatctt--gactcaactaaaacacacatcta-attgt--------agGACATGGAAATTCATGAATCACTTGGTAAAGCAGAGAAAGCACTGAAGATGAGCAAACGAAAAGATTGGTATAAGATTCTTGGAATTTCCAGAACCGCCT
















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|29663962|gb|CB660237.1|CB660237
EST:     GGGAAGGAGCGGTTCAGGATCTAAAAGAGGCTGCCCAGAAATCTCCCCAG                         GACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTA
genomic: GGGAAGGAGCGGTTCAGGATCTAAAAGAGGCTGCCCAGAAATCTCCCCAGgcaagtttta ... tcatgctcagGACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTA
EST: gi|9864967|gb|AU100717.1|AU100717
EST:     GATCTAAAAGA-GCTNCCNAG-AATCTCCCCCAG                         GACATGGGAATCCGAGAAGCACTAATGAGA-CTGAAAACCAGCTTAAGTT
genomic: GATCTAAAAGAGGCTGCCCAGAAATCT-CCCCAGgcaagtttta ... tcatgctcagGACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTT
EST: gi|29624026|gb|CB629037.1|CB629037
EST:     GGGAAGGAGCGGTTCAGGATCTAAAAGAGGCTGCCCAGAAATCTCCCCAG                         GACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTA
genomic: GGGAAGGAGCGGTTCAGGATCTAAAAGAGGCTGCCCAGAAATCTCCCCAGgcaagtttta ... tcatgctcagGACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTA
EST: gi|29685030|gb|CB681305.1|CB681305
EST:     GGGAAGGAGCGGTTCAGGATCTAAAAGAGGCTGCCCAGAAATCTCCCCAG                         GACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTA
genomic: GGGAAGGAGCGGTTCAGGATCTAAAAGAGGCTGCCCAGAAATCTCCCCAGgcaagtttta ... tcatgctcagGACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTA
EST: gi|29624027|gb|CB629038.1|CB629038
EST:     GGGAAGGAGCGGTTCAGGATCTAAAAGAGGCTGCCCAGAAATCTCCCCAG                         GACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTA
genomic: GGGAAGGAGCGGTTCAGGATCTAAAAGAGGCTGCCCAGAAATCTCCCCAGgcaagtttta ... tcatgctcagGACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTA
EST: gi|29664003|gb|CB660278.1|CB660278
EST:     GGGAAGGAGCGGTTCAGGATCTAAAAGAGGCTGCCCAGAAATCTCCCCAG                         GACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTA
genomic: GGGAAGGAGCGGTTCAGGATCTAAAAGAGGCTGCCCAGAAATCTCCCCAGgcaagtttta ... tcatgctcagGACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTA
EST: gi|58676081|gb|CK064768.1|CK064768
EST:     GGGAAGGAGCGGTTCAGGATCTAAAAGAGGCTGCCCAGAAATCTCCCCAG                         GACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTA
genomic: GGGAAGGAGCGGTTCAGGATCTAAAAGAGGCTGCCCAGAAATCTCCCCAGgcaagtttta ... tcatgctcagGACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTA
EST: gi|2310241|gb|C26396.1|C26396
EST:     GGGAAGGAGCGGTTCAGGATCTAAAAGAGGCTGCCCAGAAATCTCCCCAG                         GACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTA
genomic: GGGAAGGAGCGGTTCAGGATCTAAAAGAGGCTGCCCAGAAATCTCCCCAGgcaagtttta ... tcatgctcagGACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctgtatttttttggtacaaatgtaacagtggtttgcactgttcatgctcagGACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTAAGCAAAAGAAAAGATTGGTATAAGATCCTTGGCATTTCAAAGACGGCAT
                       atgtaac  putative branch site (score: 3)
     tgtattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgctttattagatttatctatcaaacagacttggtctctgccctttttctgtatttttttggtacaaatgtaacagtggtttgcactgttcatgctcagGACATGGGAATCCGAGAAGCACTAATGAGAGCTGAAAAGCAGCTTAAGTTAAGCAAAAGAAAAGATTGGTATAAGATCCTTGGCATTTCAAAGACGGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA