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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaattacttgcatgcattctttttttgtaggaatatctgccaagtcgtccttcactggaaactttcgtacctgactgtgatgtcctgttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g40830.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40830.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 11
------------GTGCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaattacttgcatgcattctttttttgtaggaatatctgccaagtcgtccttcactggaaactttcgtacctgactgtgatgtcctgttgcag--------
            || |||||||||||||||||||||||||||||||| |||||||| ||||||||||| ||||||| |  |  |   ||  | |  |   |  | |     ||||  | ||| |||  |   |||  |  | | |    ||   ||| |  | ||   |        
GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctgttgatat-tagtggtgcatgcttgatgcttctgtta-gtcttcc--cgtaggaggcccttg-agtaaacccagatctattattcttgcctgtctt

upper sequence: LOC_Os02g40830.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 11
------------GTGCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaa----aattacttgcatgcattctttttttgtaggaatatctgccaagtcgtccttcactggaaactttcgtacctgactgtgat-----gtcctgttgcag
            || || || ||||||||| | ||||||||||||||||||||||| || || ||||| ||||||||    ||    ||| ||| | |    |||  |  || | | | | ||   |      | |   ||   |  |||  |    ||||      |  | ||||||
GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaaaacctttggatggaattcaatttatttcgagtgtttccaaaaaggaaaaaaaatcagaaacataatacgagttgttgatcacaaatgatattgcag
















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|86867753|gb|CI342701.1|CI342701
EST:     TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|88472169|gb|CI409440.1|CI409440
EST:     TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|88295833|gb|CI532794.1|CI532794
EST:     ACCAAGGGAAGAGGATTTTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: ACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|86485479|gb|CI128112.1|CI128112
EST:     CACCAATGTTGACCAAGGGAAGAGGATTTTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: CACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|88199683|gb|CI199533.1|CI199533
EST:     GGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: GGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|88994140|gb|CI116104.1|CI116104
EST:     TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTTTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|88513774|gb|CI441280.1|CI441280
EST:     TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|88908048|gb|CI090644.1|CI090644
EST:     TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|29662111|gb|CB658386.1|CB658386
EST:     TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|88852385|gb|CI374153.1|CI374153
EST:     AGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: AGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|88247971|gb|CI247820.1|CI247820
EST:     TGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|86260441|gb|CI066314.1|CI066314
EST:     TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|88270478|gb|CI385736.1|CI385736
EST:     TGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTACTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGA
genomic: TGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATT-CTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGA
EST: gi|88261239|gb|CI364815.1|CI364815
EST:     GTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: GTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|86600560|gb|CI356317.1|CI356317
EST:     AGAGGATTCTAAAG                         GAAACTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: AGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|58679486|gb|CK068173.1|CK068173
EST:     TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACATTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|88375066|gb|CI523331.1|CI523331
EST:     CACCAATGTTGACCAAGGGAAGAGGATTTTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: CACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|88264702|gb|CI368476.1|CI368476
EST:     CCAATTTTGACCAAGGGAAGAGGATTCTAAAG                         GAAGGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: CCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|86488865|gb|CI131498.1|CI131498
EST:     ACCAATGTTGACCAAGGGAAGAGGATTTTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: ACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|13420567|gb|AU174657.1|AU174657
EST:     TTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACATTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|29689244|gb|CB685519.1|CB685519
EST:     TCGGTTGGAAGGGACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|86825242|gb|CI359932.1|CI359932
EST:     AGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: AGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|86487713|gb|CI130346.1|CI130346
EST:     TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|86489114|gb|CI131747.1|CI131747
EST:     TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|88960354|gb|CI382232.1|CI382232
EST:     CGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: CGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|58031372|gb|CX728915.1|CX728915
EST:     TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|58689592|gb|CK078279.1|CK078279
EST:     TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACATTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|29662329|gb|CB658604.1|CB658604
EST:     TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|86871574|gb|CI342373.1|CI342373
EST:     TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTCCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|89194712|gb|CI117149.1|CI117149
EST:     TTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCCTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
EST: gi|88245278|gb|CI245127.1|CI245127
EST:     TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG                         GAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaatta ... cctgttgcagGAAAGTGGAATGACCTTAATCACTGCAGAGGATCTTGATGATGCGGCTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaattacttgcatgcattctttttttgtaggaatatctgccaagtcgtccttcactggaaactttcgtacctgactgtgatgtcctgttgcag

- - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - -  GAGGAT