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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcttcattgctatatagaaccaattatcctattattgtttaggcaacaacgcatgcacataaatacagaggtacatttcgcatgcgcgattttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAG

Basic information

species Zea mays
transcript GRMZM2G036861_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036861_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------gttcttcattgctatatagaaccaattatcctattattgttta-------ggcaacaacgcat---gcacataaatacagaggta-catttcgcatgcgcgattttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAG
                                                  |  | ||   ||   || |   | |  | | | ||| ||       || | | |  | |     || | ||| |  |   | ||| |   ||   |    | || |||||||||| || || || |  ||||| ||| ||||||||||||||||||| || || || |||||||||||||||||||||| |||| |||||
gtactttttttcatgttttataatgtgtaatatagccattcattgaaccatcaactgtagtacctaaacttctcttatttgaatgtctaaaactgtggtacctaaacttctcttacttgaatgcctaaccaacatcttctatcaaccgaat-gatagGGAGGTGGAAGATCATCAGCAAGAGAGACCATTGGAAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTTAAGCTCAAATCTGGAGTAGAG
















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|148952455|gb|EC898280.2|EC898280
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAGGTGGGAG-TCGTCG
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGGAGGTCGTCG
EST: gi|148950436|gb|EC896004.2|EC896004
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
EST: gi|149096924|gb|EE182722.2|EE182722
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
EST: gi|149088025|gb|EE177228.2|EE177228
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
EST: gi|149089246|gb|EE178450.2|EE178450
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
EST: gi|149106625|gb|EE188518.2|EE188518
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
EST: gi|148951094|gb|EC896759.2|EC896759
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
EST: gi|211106358|gb|FL258167.1|FL258167
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAGGTGGGAGGTCGTCGGCCAGAGAAACCGTTTNAAGGGTGGCTGCAGGG
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
EST: gi|149084565|gb|EE174034.2|EE174034
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
EST: gi|76281790|gb|DV021358.1|DV021358
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
EST: gi|149067437|gb|EE287007.2|EE287007
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
EST: gi|149098825|gb|EE184838.2|EE184838
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
EST: gi|211106349|gb|FL258158.1|FL258158
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAAGTGGGGAGGTCGTCNGGCAGAGAA-CCGTTTGGAAGG
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGG-AGGTCGTCGGGCAGAGAAACCGTT-GGAAGG
EST: gi|148957149|gb|EC903140.2|EC903140
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
EST: gi|211106350|gb|FL258159.1|FL258159
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAGGTGGGAGGTCGTCGGGCAAAGAAACCGTTGGA
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGA
EST: gi|149071022|gb|EE159425.2|EE159425
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
EST: gi|149036977|gb|EE155215.2|EE155215
EST:     CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG                         GGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG
genomic: CTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAGgtagaatttt ... attttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacaacgcatgcacataaatacagaggtacatttcgcatgcgcgattttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAG
             acataaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttcattgctatatagaaccaattatcctattattgtttaggcaacaacgcatgcacataaatacagaggtacatttcgcatgcgcgattttgacagGGAGGTGGGAGGTCGTCGGGCAGAGAAACCGTTGGAAGGGTGGCTGCAGGGGCCCTCGCCAAGAAAATTCTTAAGCTCAAATGTGGATTAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA