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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtaatatatttaaacatgctaagtagaattgttccatattaaatgtgatctcactgggaaggttttcatacttaatggtgattcttgttttcttttcagTGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGAAGGCCACAAACACTGTCAGTTTGCCA

Basic information

species Oryza sativa
transcript LOC_Os07g48200.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G172621_T01 (Zea mays), 3'ss of exon 6
ggtaatatatttaaacatgctaagtagaattgttccatattaaatgtgatctcactgggaaggttttcatacttaatggtgattcttgttttctttt-cagTGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGAAGGCCACAAACACTGTCAGTTTGCCA
  |  |||| | ||  |||||   ||| | | |  ||| |      || ||||     |  | ||     | |      |   | | ||| | || | ||||||| |||||||| ||||| |||||||||||||||||||||||||| |||||||||||||| ||||||||| |||||
-atgctatagtaaattatgctgcatagtactatgtcatgtattccatgctctctgaatgttgtttactggaatcttctttttgtgtggttattttctgcagTGACCTTTAGTCGTATAGATCCTGGAGGGAAACTTGTTATGGGCTTTCGGAAGGCCACAAATACTGTCAGTCTGCCA

upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 6
--ggtaatatatttaaacatgctaagtagaattgttccatattaaatgtgatctcactgggaaggttttcatacttaatggtgattcttgttttctttt-cagTGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGAAGGCCACAAACACTGTCAGTTTGCCA
    |  |||| | ||  | ||| ||||| ||| |  ||| |      || ||||    ||| | | || |     |    |  || | ||| | || | ||||||| |||||||| ||||| |||||||||||||||||||||||||| |||||||||||||| ||||||||| |||||
tccatgctatagtaaattacgctgagtagtattatgtcatgtgtcccatgctctct---ggatgttgtttactggaacctttttttgtggttattttctgcagTGACCTTTAGTCGTATAGATCCTGGAGGGAAACTTGTTATGGGCTTTCGGAAGGCCACAAATACTGTCAGTCTGCCA

upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA18G05840.1 (Glycine max), 3'ss of exon 8
------ggtaatatatttaaacatgctaagtagaattgttccatattaaatgtgatctcactgggaaggttttcatacttaatggtgattcttgttttcttttcagTGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGAAGGCCACAAACACTGTCAGTTTGCCA
        || ||| |     ||  ||    | | |  ||     | | ||||  |   | |  |||  ||   || |||     |||| |||      | |  ||| || |||||||||||||| || ||||| |||||||||||||| ||| | |||||  | ||  ||     |   |  
tattggaatactatgtagggtcaaacttcacatattctttgaggctaatatgtcttgcaaatctgaaa-ttactattcttttatatgatgctt-----ttatgtagTAACATTTAGTCGGATAGATCCCGGAGGCAAACTTGTTATGGGTTTCAGAAAGGCATCTAATTCTACAGATACACAG

upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA11G31270.1 (Glycine max), 3'ss of exon 2
------ggtaatatatttaaacatgctaagtagaattgttccatattaaatgtgatctcactgggaaggttttcatacttaatggtgattcttgttttcttttcagTGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGAAGGCCACAAACACTGTCAGTTTGCCA
      | || ||| |     ||  ||    | | |  ||     | | ||||  |   | |  |||| |  |  |  || ||  |||| |||      | | |||| || |||||||||||||| |||||||| ||||| |||||||| ||| | || ||  ||||  ||     |   |  
ttattggttactatgtagggtcaaacttcagatattctttgaggctaatatgtcttgcaaatctgaagctactattcttttata-tgatgctt-----ttatgcagTAACATTTAGTCGGATAGATCCTGGAGGCAAACTAGTTATGGGTTTCAGAAAAGCATCAAATTCTACAGATACACAG

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|58671720|gb|CK060406.1|CK060406
EST:     GGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAG                         TGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTC
genomic: GGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAGgttaaatctc ... ttcttttcagTGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTC
EST: gi|58682644|gb|CK071331.1|CK071331
EST:     GGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAG                         TGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGA
genomic: GGGGGTTACACCATGCATACAATCATTACAATTACAGGCTGGTGATACAGgttaaatctc ... ttcttttcagTGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGA
EST: gi|58672846|gb|CK061532.1|CK061532
EST:     AATCATTACAATTACAGGCTGGTGATACAG                         TGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGA
genomic: AATCATTACAATTACAGGCTGGTGATACAGgttaaatctc ... ttcttttcagTGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatctcactgggaaggttttcatacttaatggtgattcttgttttcttttcagTGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGAAGGCCACAAACACTGTCAGTTTGCCA
                                     ttcttgttttcttttc  CT-rich tract
                  ttttcatacttaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtaatatatttaaacatgctaagtagaattgttccatattaaatgtgatctcactgggaaggttttcatacttaatggtgattcttgttttcttttcagTGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGAAGGCCACAAACACTGTCAGTTTGCCA

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