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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTGACATGGGTGGTGGCACCTGGGAACGTGACATGGTTGTCCGTGCTTTGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttccacgtttgataatttcttttcacaaatgcacatttctatgctgatggggaattggaaaactcatttaaagaacttatgtttttaaagagaat...

Basic information

species Oryza sativa
transcript LOC_Os06g15360.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g15360.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G035417_T01 (Zea mays), 5'ss of exon 6
TCTTGACATGGGTGGTGGCACCTGGGAACGTGACATGGTTGTCCGTGCTTTGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttccacgtttgataatttcttttcacaaatgcacatttctatgctgatggggaattggaaaactcatttaaagaacttatgtttttaaagagaat----
|||||||||||||||||| || ||||||||||| |  ||||| |||||| | ||||||||||| || ||||| ||||||||||| ||||| ||||||||||||||||  | |||  |   | |  ||| |  ||||||  || |        |  |    ||      ||||||       |||| ||| | || |  ||    
TCTTGACATGGGTGGTGGTACATGGGAACGTGATACTGTTGTTCGTGCTCTACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagttttatgtt-aactttattattttatcaatgca--ttgcagcttcattctgcctctgatgtgttcatttgtttcttttat-tttctgaaaaacatgctg
















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|29629490|gb|CB634499.1|CB634499
EST:     TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCT                         GGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
genomic: TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttcca ... catctgttagGGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
EST: gi|58682592|gb|CK071279.1|CK071279
EST:     TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCT                         GGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
genomic: TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttcca ... catctgttagGGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
EST: gi|29643232|gb|CB648239.1|CB648239
EST:     TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCT                         GGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
genomic: TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttcca ... catctgttagGGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
EST: gi|33654535|gb|CF277149.1|CF277149
EST:     TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCT                         GGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
genomic: -GCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttcca ... catctgttagGGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
EST: gi|29655833|gb|CB652108.1|CB652108
EST:     TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCT                         GGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
genomic: TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttcca ... catctgttagGGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
EST: gi|58670606|gb|CK059292.1|CK059292
EST:     TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCT                         GGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
genomic: TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttcca ... catctgttagGGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
EST: gi|58670896|gb|CK059582.1|CK059582
EST:     TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCT                         GGAATTCCTGAGAATGTGGAGCCTCCACAACCTGTGGCTCGAGCACCTGCT
genomic: TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttcca ... catctgttagGGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
EST: gi|29673854|gb|CB670129.1|CB670129
EST:     TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCT                         GGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
genomic: TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttcca ... catctgttagGGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
EST: gi|29630613|gb|CB635622.1|CB635622
EST:     TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCT                         GGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
genomic: TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttcca ... catctgttagGGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
EST: gi|29657664|gb|CB653939.1|CB653939
EST:     TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCT                         GGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
genomic: TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttcca ... catctgttagGGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
EST: gi|117226238|gb|CT846174.1|CT846174
EST:     TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCT                         GGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
genomic: TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttcca ... catctgttagGGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
EST: gi|29670071|gb|CB666346.1|CB666346
EST:     TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCT                         GGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
genomic: TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttcca ... catctgttagGGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
EST: gi|29668712|gb|CB664987.1|CB664987
EST:     TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCT                         GGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
genomic: TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttcca ... catctgttagGGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
EST: gi|29643186|gb|CB648193.1|CB648193
EST:     TGCGTGCTGCATATAACAACCCTGACAGAGCTATTGACTATCTGTATTCT                         GGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
genomic: TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttcca ... catctgttagGGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
EST: gi|29660320|gb|CB656595.1|CB656595
EST:     TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCT                         GGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
genomic: TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttcca ... catctgttagGGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
EST: gi|58596519|gb|CK007047.1|CK007047
EST:     TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCT                         GGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT
genomic: TGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttcca ... catctgttagGGAATTCCTGAGAATGTGGAGCCCCCACAACCTGTGGCTCGAGCACCTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTGACATGGGTGGTGGCACCTGGGAACGTGACATGGTTGTCCGTGCTTTGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttccacgtttgataatttcttttcacaaatgcacatttctatgctgatggggaattggaaaactcatttaaagaacttatgtttttaaagagaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT