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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGCGAGAGCACCTACGCGTTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcatcaaaagagcagttcgctagaggtttgctggtccagtttccaaagcaacagataaactgatgcccagatcgatcacctgcag

Basic information

species Zea mays
transcript GRMZM2G033828_T02
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033828_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os08g42600.2 (Oryza sativa), 5'ss of exon 17
CCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGCGAGAGCACCTACGCGTTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcatcaaaagagcagttcgctagaggtttgctggtcca-gtttccaaagcaacagataaactgatgcccagatcgatcacc-----tgcag
|||| |||||||||||||| ||||| || || || ||||| ||  | || || |||||||||||||||||||| |||| ||| |||||||||||||||||| || |  |  || |     |      ||| || |  |  |||   ||||   ||  | ||  |||||  || | | |    || |      |||||
CCCCAAGCTCCAAGAGCTATTACGCCTGTGTAGGGGAGAGTACTCATGCATTTCAGAGCCCCTCCAAGGACCTTAAGGTTATAAACAACCGCCTAAACAGgtaaaactagaaagaagctgg---aaaagaagtctttttatccttatttcactagtgagaggaaaactt-tgtctaaactattctcaatttgtgcag
















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|30086964|gb|CB885172.1|CB885172
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|76933781|gb|DV173583.1|DV173583
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|30031712|gb|CB833563.1|CB833563
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCG
EST: gi|27522004|gb|CA989110.1|CA989110
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|30087032|gb|CB885240.1|CB885240
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|30032038|gb|CB833889.1|CB833889
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|30088299|gb|CB886504.1|CB886504
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|29544714|gb|CB605094.1|CB605094
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|27575967|gb|CA998661.1|CA998661
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|166639923|gb|EG092619.1|EG092619
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGT
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGT
EST: gi|30088298|gb|CB886503.1|CB886503
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|30031776|gb|CB833627.1|CB833627
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGCGAGAGCACCTACGCGTTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcatcaaaagagcagttcgctagaggtttgctggtccagtttccaaagcaacagataaactgatgcccagatcgatcacctgcag

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