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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGGTTGCGCCGTCTGGGTTAAAGAACAGCAGTAGCACCAGCATGGGTGCTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctatcatgatgagaagtttaatttcttccatgtgccatgtaaatttgactttgttgtaacatgtcgaactgaatggtaaatccag

Basic information

species Oryza sativa
transcript LOC_Os01g14860.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14860.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G835235_T04 (Zea mays), 5'ss of exon 2
AGGGGTTGCGCCGTCTGGGTTAAAGAACAGCAGTAGCACCAGCATGGGTGCTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgt-aagtct-------atcatgatgagaagttt----aatttcttccatgtgccatgtaaatttg-actttgttgtaacatgtcgaactgaatggtaaatccag
 || ||||| || |||||||  ||||||||||| ||||||||||| ||||| || |||||||  ||||| ||| | || || ||||| || || |||||||| |||  |       ||| || |      |||    ||||||||| |  |    || ||| ||| ||  || |||| ||| | ||  ||||||| ||||||||
TGGTGTTGCCCCTTCTGGGTACAAGAACAGCAGCAGCACCAGCATTGGTGCCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattcattggcatcttgtttcaggctttctgtaatttcttcaagattatgtgaaaaattggaccgtgatgtagcat-ttgacatgaatggcaaatccag
















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|58602831|gb|CK013359.1|CK013359
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|58685932|gb|CK074619.1|CK074619
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|58661642|gb|CK050322.1|CK050322
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|58598975|gb|CK009503.1|CK009503
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|58674441|gb|CK063127.1|CK063127
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|58665294|gb|CK053980.1|CK053980
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|58676495|gb|CK065182.1|CK065182
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|58665103|gb|CK053789.1|CK053789
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|29687086|gb|CB683361.1|CB683361
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|58664372|gb|CK053058.1|CK053058
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|58673516|gb|CK062202.1|CK062202
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|58671331|gb|CK060017.1|CK060017
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|58657986|gb|CK046666.1|CK046666
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAGCAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|58590979|gb|CF989287.1|CF989287
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGCAAA-CGGCCACAT
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAG-AAACCGGCCACAT
EST: gi|58653056|gb|CK041736.1|CK041736
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTAGGGACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|29618976|gb|CB623988.1|CB623988
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|58653567|gb|CK042247.1|CK042247
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGACACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|163921584|gb|EG712155.1|EG712155
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|86596734|gb|CI286647.1|CI286647
EST:     CCGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
EST: gi|33796677|gb|CF324206.1|CF324206
EST:     CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAG                         GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA
genomic: CTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctat ... gtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGGTTGCGCCGTCTGGGTTAAAGAACAGCAGTAGCACCAGCATGGGTGCTGAGAAGTTGCCTGATCAGATGCATGATCTGAAGATAAGGGACGATAAGgtaagtctatcatgatgagaagtttaatttcttccatgtgccatgtaaatttgactttgttgtaacatgtcgaactgaatggtaaatccag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA