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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACAAGGTGGTGAAGATCCAGCTCCACCCCACGCACCCCTGGCTCGTCACCGCCGACGCCAACGACCGCGTCTCCGTCTGGGACTGGGAGCACCGCCAGgtaccgctttccgcgagagatcccgtggggatagacccctgcctctgttttttttcttgtccgtttgatctcgtcgtgccggaaaaggcatcttcgtgagctctgtttgcgattgaattgacctcgactggtgttggaatttgtgtggtgttag

Basic information

species Oryza sativa
transcript LOC_Os01g46510.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g46510.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G000177_T01 (Zea mays), 5'ss of exon 1
CGACAAGGTGGTGAAGATCCAGCTCCACCCCACGCACCCCTGGCTCGTCACCGCCGACGCCAACGACCGCGTCTCCGTCTGGGACTGGGAGCACCGCCAGgtaccgctttccgcgagagatcccgtggggatagacccctgcctctgttttttttcttgtccgtttgatctcgtcgtgccggaaaaggcatcttcgtgagctctgtttgcgattgaattgacctcgactggtgttggaatttgtgtggtgttag
|||||| || ||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||| |||||| |||||||||||||||||||||||||| |    || || |   | |  ||                         ||   |||||||| ||   | | |  |       |||||  |||| |||||| |    | |||| |||     |  ||| |||  ||  |       
CGACAAAGTCGTGAAGATCCAGCTCCACCCCACTCACCCCTGGCTCGTCACCGCGGACGCCAACGACCGCGTCTCTGTCTGGAACTGGGAGCACCGCCAGgtaccgcttgcttttagggaccttctagcaat------------------------ctgcttgtttgatcccgcgatacagagagg-----cttcg-aagctttgtttggggcccatttgatctcacggtgctttgtaatccgttag-------
















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|88719571|gb|CI743081.1|CI743081
EST:     CCGCCGACGCCAACGACCGCGTCTCCGTCTGGGACTGGGAGCACCGCCAG                         GTGATCTACGAGCTGAAGGCGGGTGGCGTGGACGAGCGGCGGTTGGTTGGA
genomic: CCGCCGACGCCAACGACCGCGTCTCCGTCTGGGACTGGGAGCACCGCCAGgtaccgcttt ... gtggtgttagGTGATCTACGAGCTGAAGGCGGGTGGCGTGGACGAGCGGCGGTTGGTTGGA
EST: gi|88301497|gb|CI597190.1|CI597190
EST:     CCGCCGACGCCAACGACCGCGTCTCCGTCTGGGACTGGGAGCAACGCCAG                         GTGATCTACGAGCTGAAGGCGGGTGGCGTGGACGAGCGGCGGTCGGTTGGA
genomic: CCGCCGACGCCAACGACCGCGTCTCCGTCTGGGACTGGGAGCACCGCCAGgtaccgcttt ... gtggtgttagGTGATCTACGAGCTGAAGGCGGGTGGCGTGGACGAGCGGCGGTTGGTTGGA
EST: gi|88826572|gb|CI777137.1|CI777137
EST:     CCGCCGACGCCAACGACCGCGTCTCCGTCTGGGACTGGGAGCACCGCCAG                         GTGATCTACGAGCTGAAGGCGGGTGGCGTGGACGAGCGGCGGTTGGTTGGA
genomic: CCGCCGACGCCAACGACCGCGTCTCCGTCTGGGACTGGGAGCACCGCCAGgtaccgcttt ... gtggtgttagGTGATCTACGAGCTGAAGGCGGGTGGCGTGGACGAGCGGCGGTTGGTTGGA
EST: gi|88315291|gb|CI613560.1|CI613560
EST:     CCGCCGACGCCAACGACCGCGTCTCCGTCTGGGACTGGGAGCACCGCCAG                         GTGATCTACGAGCTGAAGGGGGGTGGCGTGGACGAGCGGCGGTTGGTTGGA
genomic: CCGCCGACGCCAACGACCGCGTCTCCGTCTGGGACTGGGAGCACCGCCAGgtaccgcttt ... gtggtgttagGTGATCTACGAGCTGAAGGCGGGTGGCGTGGACGAGCGGCGGTTGGTTGGA
EST: gi|88447491|gb|CI584606.1|CI584606
EST:     CCGCCGACGCCAACGACCGCGTCTCCGTCTGGGACTGGGAGAACCGCCAG                         GTGATCTACGAGCTGAAGGCGGGTGGCGTGGACGAGCGGCGGTTGGTTGGA
genomic: CCGCCGACGCCAACGACCGCGTCTCCGTCTGGGACTGGGAGCACCGCCAGgtaccgcttt ... gtggtgttagGTGATCTACGAGCTGAAGGCGGGTGGCGTGGACGAGCGGCGGTTGGTTGGA
EST: gi|88405955|gb|CI591350.1|CI591350
EST:     CCGCCGACGCCAACGACCGCGTCTCCGTCTGGGACTGGGAGCACCGCCAG                         GTGATCTACGAGCTGAAGGCGGGTGGCGTGGACGAGCGGCGGTTGGTTGGA
genomic: CCGCCGACGCCAACGACCGCGTCTCCGTCTGGGACTGGGAGCACCGCCAGgtaccgcttt ... gtggtgttagGTGATCTACGAGCTGAAGGCGGGTGGCGTGGACGAGCGGCGGTTGGTTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGACAAGGTGGTGAAGATCCAGCTCCACCCCACGCACCCCTGGCTCGTCACCGCCGACGCCAACGACCGCGTCTCCGTCTGGGACTGGGAGCACCGCCAGgtaccgctttccgcgagagatcccgtggggatagacccctgcctctgttttttttcttgtccgtttgatctcgtcgtgccggaaaaggcatcttcgtgagctctgtttgcgattgaattgacctcgactggtgttggaatttgtgtggtgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA