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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAATCAGACGCAGGTCTACTCCACCAATGCCAACTCTGGTAGCAATGGCGTCTTCGTCGGGATTACGCTCATCCAGTCGGCGGCCGCCAAGGGAGCCGgtatatatgtttccttgttccctgaattgttcgttcattccttgattctagtattttttttccggctgcaaagattgcttttttattggccttgccttgc...

Basic information

species Oryza sativa
transcript LOC_Os07g44070.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g44070.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G160569_T02 (Zea mays), 5'ss of exon 1
CTGAATCAGACGCAGGTCTACTCCACCAATGCCAACTCTGGTAGC---AATGGCGTCTTCGTCGGGATTACGCTCATCCAGTCGGCGGCCGCCAAGGGAGCCGgtatatatgtttccttgttccctgaattgttcgttcattccttgattctagtattttttttccggctgcaaagattgcttttttattggcctt-gccttgc
   ||  |||| ||||| ||| ||||||  |||||||| ||| ||   || ||||||||||||||  | |||||||||||||||||||| ||||||||||| |||| ||   | |  ||    |       |   | |  | || | |||  |    | | | |   | ||| |||| |  |||||| ||  |    |||  ||
---AACGAGACACAGGTGTACGCCACCACCGCCAACTCCGGTGGCGGCAACGGCGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgta-attcctctggttccagctcctgcagcgggattgtgccattatttaatctgtatatattttgttgcgaagactagtttttttttatcagcagccacgc
















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|88355781|gb|CI626222.1|CI626222
EST:     CGTCTTCGTCGGGATTACGCTCATCCAGTCGGCGGCCGCCAAGGGAGCCG                         TATGCTTGGATGGGAGCTTACCAGGGTATCACCTACACCGAGGGTTTGGAT
genomic: CGTCTTCGTCGGGATTACGCTCATCCAGTCGGCGGCCGCCAAGGGAGCCGgtatatatgt ... atcatggcagTATGCTTGGATGGGAGCTTACCAGGGTATCACCTACACCGAGGGTTTGGAT
EST: gi|58669941|gb|CK058627.1|CK058627
EST:     CGTCTTCGTCGGGATTACGCTCATCCAGTCGGCGGCCGCCAAGGGAGCCG                         TATGCTTGGATGGGAGCTTACCAGGGTATCACCTACACCGAGGGTTTGGAT
genomic: CGTCTTCGTCGGGATTACGCTCATCCAGTCGGCGGCCGCCAAGGGAGCCGgtatatatgt ... atcatggcagTATGCTTGGATGGGAGCTTACCAGGGTATCACCTACACCGAGGGTTTGGAT
EST: gi|88343238|gb|CI627198.1|CI627198
EST:     CGTCTTCGTCGGGATTACGCTCATCCAGTCGGCGGCCGCCAAGGGAGCCG                         TATGCTTGGATGGGAGCTTACCAGGGTATCACCTACACCGAGGGTTTGGAT
genomic: CGTCTTCGTCGGGATTACGCTCATCCAGTCGGCGGCCGCCAAGGGAGCCGgtatatatgt ... atcatggcagTATGCTTGGATGGGAGCTTACCAGGGTATCACCTACACCGAGGGTTTGGAT
EST: gi|88367213|gb|CI563977.1|CI563977
EST:     CGTCTTCGTCGGGATTACGCTCATCCAGTCGGCGGCCGCCAAGGGAGCCG                         TATGCTTGGATGGGAGCTTACCAGGGTATCACCTACACCGAGGGTTTGGAT
genomic: CGTCTTCGTCGGGATTACGCTCATCCAGTCGGCGGCCGCCAAGGGAGCCGgtatatatgt ... atcatggcagTATGCTTGGATGGGAGCTTACCAGGGTATCACCTACACCGAGGGTTTGGAT
EST: gi|58689727|gb|CK078414.1|CK078414
EST:     CGTCTTCGTCGGGATTACGCTCATCCAGTCGGCGGCCGCCAAGGGAGCCG                         TATGCTTGGATGGGAGCTTACCAGGGTATCACCTACACCGAGGGTTTGGAT
genomic: CGTCTTCGTCGGGATTACGCTCATCCAGTCGGCGGCCGCCAAGGGAGCCGgtatatatgt ... atcatggcagTATGCTTGGATGGGAGCTTACCAGGGTATCACCTACACCGAGGGTTTGGAT
EST: gi|5003056|gb|AU068165.1|AU068165
EST:     CAAGGGAGCCG                         TATGCTTGGATGGGAGCTTACCAGGGTATCACCTACACCGAGGGTTTGGAT
genomic: CAAGGGAGCCGgtatatatgt ... atcatggcagTATGCTTGGATGGGAGCTTACCAGGGTATCACCTACACCGAGGGTTTGGAT
EST: gi|58596473|gb|CK007001.1|CK007001
EST:     CGTCTTCGTCGGGATTACGCTCATCCAGTCGGCGGCCGCCAATGGAGCCG                         TATGCTTGGATGGGAGCTTACCAGTGTATCACCTACACCGAGGGTTTGGAT
genomic: CGTCTTCGTCGGGATTACGCTCATCCAGTCGGCGGCCGCCAAGGGAGCCGgtatatatgt ... atcatggcagTATGCTTGGATGGGAGCTTACCAGGGTATCACCTACACCGAGGGTTTGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAATCAGACGCAGGTCTACTCCACCAATGCCAACTCTGGTAGCAATGGCGTCTTCGTCGGGATTACGCTCATCCAGTCGGCGGCCGCCAAGGGAGCCGgtatatatgtttccttgttccctgaattgttcgttcattccttgattctagtattttttttccggctgcaaagattgcttttttattggccttgccttgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cggctgc