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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgttttttgaacattggcatgcaactatcaacatttttgtgtatttattttctgtgcatgcttatttacctccatgtttcttgcataccaaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG

Basic information

species Zea mays
transcript GRMZM2G030902_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030902_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 3
-----tcgttttttgaacattggcatgcaactatcaacatttttgtgtatttattttctgtgcatgcttatttacctccatgtttcttgcataccaaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG
     |   || || |  | ||      |   |||||  | || |  |  ||   |  | ||  | || | | ||| | || ||||||| |    ||||| | ||||||| || ||||| ||||||||||||||||| |||||||| ||| ||||||| || ||||| |||
ttaaataacttcttcagtactg-----tattcatcaatttattagcctgatttggtaatttgtgtactgactgaccactatctttcttgtacgttaaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG
















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|211347523|gb|FL007072.1|FL007072
EST:     AGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGGAAG                         GAGCGGTCTTCTGGG
genomic: AGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATG-AAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGG
EST: gi|148936779|gb|EC880917.2|EC880917
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|149104347|gb|EE289792.2|EE289792
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|31664299|gb|CD573024.1|CD573024
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|22545757|gb|BU098131.1|BU098131
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|71769697|gb|DR967634.1|DR967634
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211345125|gb|FL007061.1|FL007061
EST:     AGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATTGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATC
genomic: AGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCAT-GAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATC
EST: gi|148955713|gb|EC901400.2|EC901400
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211345133|gb|FL007069.1|FL007069
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|87156149|gb|DY400938.1|DY400938
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211345132|gb|FL007068.1|FL007068
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|149096474|gb|EE182216.2|EE182216
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|149000018|gb|EE037116.2|EE037116
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211345131|gb|FL007067.1|FL007067
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|6564152|gb|AW231774.1|AW231774
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|149104935|gb|EE290405.2|EE290405
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211345130|gb|FL007066.1|FL007066
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGG
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGG
EST: gi|26558833|gb|CA831068.1|CA831068
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|22473110|gb|BU037590.1|BU037590
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|71304925|gb|DR788593.1|DR788593
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211345135|gb|FL007071.1|FL007071
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAA                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211345122|gb|FL007058.1|FL007058
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTC
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTC
EST: gi|31557986|gb|CD527198.1|CD527198
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211138007|gb|FL213712.1|FL213712
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211345128|gb|FL007064.1|FL007064
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|32919564|gb|CF024376.1|CF024376
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|149080743|gb|EE169805.2|EE169805
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|21432115|gb|BQ547605.1|BQ547605
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|9952229|gb|BE638812.1|BE638812
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGTGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|13558465|gb|BG549821.1|BG549821
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211345127|gb|FL007063.1|FL007063
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCT
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCT
EST: gi|60350487|gb|DN217460.1|DN217460
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA
EST: gi|211345129|gb|FL007065.1|FL007065
EST:     GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAG                         GAACGGCCTTCTGGGCGATCTCGTGGGCTTGGCTATGTACCTTTCGCATCA
genomic: GAGAGTACATGGCCAAGTTTGGACCCCTAGATGATTGTGTCGTCATGAAGgtttgccata ... aaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttctgtgcatgcttatttacctccatgtttcttgcataccaaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG
                                             aaaataaca  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgttttttgaacattggcatgcaactatcaacatttttgtgtatttattttctgtgcatgcttatttacctccatgtttcttgcataccaaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG