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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACGACGGACAGACGGATCTGCTGCACTCGTACGGGCTAGGGTATCCCGAGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgtcgtcgtctcgtccctgtcgaccctccccactgcccccgagtcccagtctcccagactgagtcgcctcacgtggcgtgccgttgggtttgtctgtcctgcctgcag

Basic information

species Zea mays
transcript GRMZM2G030712_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030712_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g05480.1 (Oryza sativa), 5'ss of exon 7
CGACGACGGACAGACGGATCTGCTGCACTCGTACGGGCTAGGGTATCCCGAGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgtcgtcgtctcgtccc--tgtcgaccctccccactgcc---cccgagtccca-gtctcccagactgagtcgcctcacgtggcgtgccgttgggtttgtctgtcctgcctgcag
 |||||  |  |||  ||| ||| || ||| ||||||||||| || || || ||||||||||| ||||| |||||||||||||||||||||||||| |||||||||      | |  ||||  |  || |    |    ||| | |   || ||     |  | | |     | ||    |  |    |  | |   || |||||  | | | |       
GGACGAAAGGGAGAGAGATTTGCAGCTCTCCTACGGGCTAGGATACCCTGAACCCAACGTCGTGTTCGCTCTGTGCAGAGGCAGCCGCTCCTCGCCTGCAgtacgtacaatcttgaatcgtttcattggcagatcgaaacacagtctttcctgaacaaaatattttcattgttcagaattcagattaagaattcttgtgtgtttggatttgcag-------
















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|211056577|gb|FL481911.1|FL481911
EST:     GCCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCCCCAGCA                         CTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
genomic: G-CCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
EST: gi|149027590|gb|EE046581.2|EE046581
EST:     AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCA                         CTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
genomic: AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
EST: gi|29130825|gb|CB381529.1|CB381529
EST:     AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCA                         CTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
genomic: AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
EST: gi|60399493|gb|DN232305.1|DN232305
EST:     AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCA                         CTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
genomic: AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
EST: gi|28930819|gb|CB334180.1|CB334180
EST:     AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCA                         CTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
genomic: AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
EST: gi|29129867|gb|CB380571.1|CB380571
EST:     CAGCCGCTCCTCGCCAGCA                         CTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
genomic: CAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
EST: gi|30306390|gb|CD001063.1|CD001063
EST:     AACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCA                         CTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
genomic: AACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
EST: gi|78114752|gb|DV533140.1|DV533140
EST:     AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCA                         CTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG
genomic: AGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgt ... ctgcctgcagCTGCGCGTGTACACGGCGGAGGACGTGTCGAACGAGCTGGAGCGGGCCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGACGACGGACAGACGGATCTGCTGCACTCGTACGGGCTAGGGTATCCCGAGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCTCCTCGCCAGCAgtacgtgtgtcgtcgtctcgtccctgtcgaccctccccactgcccccgagtcccagtctcccagactgagtcgcctcacgtggcgtgccgttgggtttgtctgtcctgcctgcag

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