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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCCTGCAAAATAGCCGGACGCAACATCAACGCCGCCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAGgtatgagcaaggacgcatgattaggtccaaacccggctgaaagcacgatgctcctactgtactgattgtatgcctccacacacacaggcatgctaatttcagcttcggcccttttaatgcag

Basic information

species Zea mays
transcript GRMZM5G843914_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G843914_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g55890.1 (Oryza sativa), 5'ss of exon 10
GCTGCCTGCAAAATAGCCGGACGCAACATCAACGCCGCCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAGgtatgagcaaggacgcatgattaggtccaaacccggctgaaagcacgatgctcctactgtactgattgtatgcctccacacacacaggcatgctaatttca-gcttcggcccttttaatgcag
|||||||||||||| || ||||| | |||||| |  || || ||||||||||| |||||||| ||||||||| |||| || |||||||||  |||||  | | || |||||||| ||||   | | ||||    ||  ||  |||||||||||| |||             || |||||||||||  | |  | |  |||||||||||||
GCTGCCTGCAAAATTGCTGGACGGAGCATCAATGTAGCTGTTATCCAGAGCATGGTTCTTGGATGCAACACATACTGTCCTGGACAGgta-aagcaaacatg-attattaggtcaaaact-agttaaaagtgtaatattcacactgtactgattatata-----------gcaagcatgctaattctatgtgttgttccttttaatgcag
















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|71431420|gb|DR812470.1|DR812470
EST:     CCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAG                         TGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
genomic: CCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAGgtatgagcaa ... tttaatgcagTGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
EST: gi|74241581|gb|DT649495.1|DT649495
EST:     CCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAG                         TGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
genomic: CCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAGgtatgagcaa ... tttaatgcagTGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
EST: gi|71431421|gb|DR812471.1|DR812471
EST:     CCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAG                         TGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
genomic: CCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAGgtatgagcaa ... tttaatgcagTGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
EST: gi|88756881|gb|DY541022.1|DY541022
EST:     CCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAG                         TGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
genomic: CCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAGgtatgagcaa ... tttaatgcagTGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
EST: gi|89760782|gb|DY689054.1|DY689054
EST:     CCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAG                         TGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
genomic: CCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAGgtatgagcaa ... tttaatgcagTGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
EST: gi|78123668|gb|DV542052.1|DV542052
EST:     CCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAG                         TGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
genomic: CCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAGgtatgagcaa ... tttaatgcagTGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
EST: gi|60357556|gb|DN224529.1|DN224529
EST:     CCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAG                         TGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
genomic: CCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAGgtatgagcaa ... tttaatgcagTGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
EST: gi|101391015|gb|EB817443.1|EB817443
EST:     CGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCCGGACAG                         TGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
genomic: CGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCC-GGACAGgtatgagcaa ... tttaatgcagTGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
EST: gi|211041651|gb|FL024100.1|FL024100
EST:     CCGTCATCCAGAGCATTGTTCTTGGATGCAACACACACTGCCCCGGACAG                         TGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG
genomic: CCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAGgtatgagcaa ... tttaatgcagTGGCTACGGACGCTGCTTTACCCCAGGATCAAAAGCAAGGTGAGCAAAGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCCTGCAAAATAGCCGGACGCAACATCAACGCCGCCGTCATCCAGAGCATTGTTCTTGGGTGCAACACACACTGCCCCGGACAGgtatgagcaaggacgcatgattaggtccaaacccggctgaaagcacgatgctcctactgtactgattgtatgcctccacacacacaggcatgctaatttcagcttcggcccttttaatgcag

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