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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAATCATAATTTGTTCCAAAAATTCTAATGGTATTTATTTTTGACTTATCAATACAGGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgccttagttcaactataattatttctggaactaattgttttttaaattgttcttggaaattgcatttaagttcccttcactatttgaaattcgctggcaatctttagtgtggcccaatatttatgtattagttccttaatactctgctggtatttgctcctgtag

Basic information

species Oryza sativa
transcript LOC_Os09g07830.3
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07830.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM5G830250_T01 (Zea mays), 5'ss of exon 10
GTAATCATAATTTGTTCCAAAAATTCTAATGGTATTTATTTTTGACTTATCAATACAGGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagc--tgccttagttcaactataattatttctggaactaattgttttttaaattgttcttggaaattgcatttaagttcccttcactatttgaaattcgctggcaatctttagtgtggcccaatatttatgtattagttccttaatactctgctggtatttgctcctgtag
                                                          |||||||||||||||||||||||||| ||||||||||||||||||||      |||   | |||||  ||| ||| ||||  | |    |    | ||   | |   |   ||||||         ||   ||||||  || |    ||||  | || |   ||   | |      || || |  ||  |    ||   ||||| ||  | || ||
----------------------------------------------------------GCTGTTGCACTTGCAAATCAAAAGCTCCTTGGAATTCCTTCAgtaagtgtcatctttactaaactaccattctttgtggattttaaaagtcaaaacatcactttcata---tgcattcg---ctatttttttatttgctatgcagcagcaacatgtaatc--gcatgaca-----atagtattctctcta----ctaacggtatatgtgcgtgcag

upper sequence: LOC_Os09g07830.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM5G866758_T02 (Zea mays), 5'ss of exon 12
GTAATCATAATTTGTTCCAAAAATTCTAATGGTATTTATTTTTGACTTATCAATACAGGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagc--tgccttagttcaactataattatttctggaactaattgttttttaaattgttcttggaaattgcat-ttaagttcccttcactatttgaaattcgctggcaatctttagtgtggcccaatatttatgtattagttccttaatactctgctggtatttgctcctgtag
                                                          |||||||| |||||||||||||| |||||||||||||||||||||||     |||   || ||||   ||| ||| ||||  | |    ||    |||   | |  |||| | ||| ||   |    ||   ||||||  || |    ||||  | || |      || |||    ||||||  ||  ||     ||    | || ||    || ||
----------------------------------------------------------GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCAgtaagtgtcacctgtattaaactgccattctttgtggattttagaagttaaacaatcactttcagaaagtacatattgtctcttttttgttatttgctatgcagcagcaacgtgtaat----tgcattataacagtatta--tctgta-----ctaacagcatatgtgtttgcag

upper sequence: LOC_Os09g07830.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G085474_T04 (Zea mays), 5'ss of exon 12
GTAATCATAATTTGTTCCAAAAATTCTAATGGTATTTATTTTTGACTTATCAATACAGGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaag---ctgccttagttcaactataattatttctg---gaact-aattgttttttaaattgttcttggaaattgcatttaagttcccttcactatttgaaattcgctggcaatctttagtgtggcccaatatttatgtattagttccttaatactctgctggtatttgctcctgtag
                                                          ||||| |||||||||||||||||||||||||| ||||||||||||||   | ||     || | || | |||  |||||   ||||| ||  |  |   |  |  ||||  |||| ||||  |   |||  ||     | ||                                                                               
----------------------------------------------------------GCTGTCGCACTTGCAAATCAAAAGCTTCTTGGGATTCCTTCAgtaagtgcccgctgatattgagctttcatttcttctgtgtgaacttaaaagcctaaaatgtcattctcagaaagtgcaccttgattct-tttgtggtgtgc------------------------------------------------------------------------------

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|88265504|gb|CI376406.1|CI376406
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTA-GACATCCTCTT-GA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88462858|gb|CI519770.1|CI519770
EST:     CTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: CTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|86536502|gb|CI176708.1|CI176708
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88267020|gb|CI378955.1|CI378955
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88468140|gb|CI517599.1|CI517599
EST:     TTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: TTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88267537|gb|CI379472.1|CI379472
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAATCATAATTTGTTCCAAAAATTCTAATGGTATTTATTTTTGACTTATCAATACAGGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgccttagttcaactataattatttctggaactaattgttttttaaattgttcttggaaattgcatttaagttcccttcactatttgaaattcgctggcaatctttagtgtggcccaatatttatgtattagttccttaatactctgctggtatttgctcctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT