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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCAGAATGGTTCAGAACGGTGATATAGTTTTTAATAAAGTATTTGTCCCTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatatttcatagcattttcgcttatactgatacattaacatgttgcatagagtaatccagtcctggtaccaacttttgagtgcccaaacag

Basic information

species Oryza sativa
transcript LOC_Os01g06600.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06600.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G862219_T02 (Zea mays), 5'ss of exon 9
TCTCAGAATGGTTCAGAACGGTGATATAGTTTTTAATAAAGTATTTGTCCCTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatatttcatagcattttcgcttatactgatacattaacatgttgcatag--agtaatccagtcctggt-accaacttttga-gtgcccaaacag
 ||||| ||||||||||||||||| |||||||| || || || || |||||||| ||||| ||  |||||||  |||| || |||||||| || |||||||||  |      ||   |  || || || | ||  | |  |  ||   |  |      || ||  |   ||| |  || | | |    |||  ||| |||
CCTCAGGATGGTTCAGAACGGTGACATAGTTTTGAACAAGGTGTTCGTCCCTGACGAAGACCGGTTGCCAGGCATCAACTCGTTTCAGGACATCAGCAAGgtaccggc----caacactcttccgattctgcttctgccgtgccaaactataagctcggtgatgtaaatctgcttgcctattctcactgtgtgcaagcag
















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|29666427|gb|CB662702.1|CB662702
EST:     CTGAGGGAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GGTCCTTGCTATTTC
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagG-TCCTTGCTATTTC
EST: gi|29666426|gb|CB662701.1|CB662701
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|14713699|gb|AU197670.1|AU197670
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|33683998|gb|CF312237.1|CF312237
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTG
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTG
EST: gi|88344179|gb|CI654609.1|CI654609
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGCCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|13165132|gb|AU173929.1|AU173929
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|56157778|gb|C26441.2|C26441
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|29660291|gb|CB656566.1|CB656566
EST:     AGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: AGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|29678764|gb|CB675039.1|CB675039
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCAGAATGGTTCAGAACGGTGATATAGTTTTTAATAAAGTATTTGTCCCTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatatttcatagcattttcgcttatactgatacattaacatgttgcatagagtaatccagtcctggtaccaacttttgagtgcccaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG