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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaatgaatgagctttctctgcctagaattcttcggcaaatgtggaaaccccaagttgtggcctttgagtctttgagttttagtacaattaaat...

Basic information

species Zea mays
transcript GRMZM2G095348_T02
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 23
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 24
---GCATCGGAAGAGAA-GGAAATGCA--TAACACAGATGATGCTGATGAACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaatgaatgagctttctctgccta---gaattcttcggcaaatgtggaaaccccaagtt-gtggcctttgagtctttgagttttagtacaattaaat
     |  ||| ||||    | ||| |  |  |  || |||||||||||| | ||||||||| |||   ||||||||||| |||||||||||||||  ||||||| |||||||| || |||  || |||||   ||||| || ||||| |||  |||||| || || ||   |  ||| ||  |   |||     ||| |    
AACAAAGTGGAGGAGAGCACAGATGAAGCTGTCGAAGTTGATGCTGATGAGCCTGAAGAGACCGTTCTTGTAAATGGGAAAGAGGGTGAGGAACAGTGGGgtacgaacaatgaaggaacttcgtcagcctaaaagaattgtttggcaagtgtaaaaacccaaattttgtctgcggtgattcactagctttgcccccaaat----

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 23
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 24
GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaatgaatgagctttctctgccta---gaattcttcggcaaatgtggaaaccccaagtt-----gtggcctttga--------gtctttgagttttagtacaattaaat----------------------------
                                      |||||| | ||||||||| |||   ||||||||||| |||||||||||||||  ||||||| |||||||| || |||  || |||||   ||||| || ||||| |||  |||||| || ||     | ||   || |        | |    | || ||| ||  || ||                             
--------------------------------------TGATGAGCCTGAAGAGACCGTTCTTGTAAATGGGAAAGAGGGTGAGGAACAGTGGGGTACGAACAATGAAGGAACTTCGTCAGCCTAAAAGAATTGTTTGgcaagtgtaaaaacccaaattttgtctgcggtgattcactagctttgcccccaaattataggactgttgaacctttctagtacttcagtttttgaaaaag
















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|32856876|gb|CD996557.1|CD996557
EST:     GGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: GGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|32839442|gb|CD979123.1|CD979123
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|60345624|gb|DN212597.1|DN212597
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|32846872|gb|CD986553.1|CD986553
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|60347180|gb|DN214153.1|DN214153
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|211347064|gb|FK984260.1|FK984260
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|32934584|gb|CF039396.1|CF039396
EST:     AGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: AGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|113841925|gb|DW968155.1|DW968155
EST:     AGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: AGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|71443012|gb|DR824062.1|DR824062
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|6681776|gb|AW287763.1|AW287763
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCNCAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|6563651|gb|AW231378.1|AW231378
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAAGGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaatgaatgagctttctctgcctagaattcttcggcaaatgtggaaaccccaagttgtggcctttgagtctttgagttttagtacaattaaat

- - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA