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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTGCGCCTTCCCCGTCTGCCGGGACTGCTACGAATACGAGCGCCGGGAGGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtccccaaccccatccaccgaaatgcagctccactaccctggcgctaatgcattagtcgggcggcattcgatgattcttctttagtctcaattgcccactcagctcggtcctatgcgccggactttgtttgcag

Basic information

species Zea mays
transcript GRMZM2G025231_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025231_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g24190.1 (Oryza sativa), 5'ss of exon 2
GAGTGCGCCTTCCCCGTCTGCCGGGACTGCTACGAATACGAGCGCCGGGAGGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtccccaaccccatccaccgaaatgcagct--ccactaccctggcgctaatgcattagtcgggcggc-attcgat-gattcttctttagtctcaattgcccactcagctcggtcctatgcgccggactttgtttgcag
|||||||||||||| || ||||| ||||||||||| ||||||||||| |||||||||||||||||||||||||||||||| || | ||||||||||| |||   ||  | ||  |     | |       |||  |  || |  ||||  | |    || |   ||   |      ||  | |||||  |  |  ||   |||||                                       
GAGTGCGCCTTCCCGGTGTGCCGCGACTGCTACGAGTACGAGCGCCGCGAGGGCACGCAGAACTGCCCCCAGTGCAAGACCCGCTTCAAGCGCCTCAGGGgcaagtcacacccgcaatgccgaattggtggcaatttgccccccccctcccccccccgcctagttcccccaattgctcactcgattcgcccctgatcgatattgcag-------------------------------------
















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|149001186|gb|EE038454.2|EE038454
EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGG                         GCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
EST: gi|211344801|gb|FL219951.1|FL219951
EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGG                         GCTGCCAGCGTGTGACCGGTGACGAGGAGGAAGACGGCGTCGATGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
EST: gi|211344804|gb|FL219954.1|FL219954
EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGG                         GCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
EST: gi|71309263|gb|DR790918.1|DR790918
EST:     GCACGCAAAACTGCCCCCCAGTGCAAGACTCGATACAAGCGCCCTCAAGG                         GCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTG
genomic: GCACGCAGAACTGCCCCC-AGTGCAAGACTCGATACAAGCGCC-TCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTG
EST: gi|211344807|gb|FL219957.1|FL219957
EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGG                         GCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
EST: gi|211342416|gb|FL219947.1|FL219947
EST:     GGCACGCAGAACTTGCCCCCCGTGCAAGACTCGATACAAGCCCCTCAAGG                         GCTGCCCAGCGTGTGA
genomic: GGCACGCAGAACT-GCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCC-AGCGTGTGA
EST: gi|211344805|gb|FL219955.1|FL219955
EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGG                         GCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCTATGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
EST: gi|211342409|gb|FL219940.1|FL219940
EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGG                         GCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
EST: gi|211342413|gb|FL219944.1|FL219944
EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGG                         GCTGCCAGCGTGTGACCGGTGACGAGGAGGGAG-ACGGCGTCNATGACCTG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGG-AGGACGGCGTCGATGACCTG
EST: gi|211489169|gb|FL444477.1|FL444477
EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGG                         GCTGCCAGCGTGTGACCGCTGACGAGGAGGAGGACGGCGTCGATGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTGCGCCTTCCCCGTCTGCCGGGACTGCTACGAATACGAGCGCCGGGAGGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtccccaaccccatccaccgaaatgcagctccactaccctggcgctaatgcattagtcgggcggcattcgatgattcttctttagtctcaattgcccactcagctcggtcctatgcgccggactttgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA