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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcctaacataatgctctggcgtctggattgactctgctgcaatcctcatttctctatccaatagctacctctggtaacataatttccatccgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGGATGTGGGTGGGCAAGAAAAACTCAGGTCACTGTGGAAGATGTACCTGAG

Basic information

species Zea mays
transcript GRMZM2G152929_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152929_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g03610.1 (Oryza sativa), 3'ss of exon 2
----gcctaacataatgctc--tggcgtctggattgactctgctgcaatcctcatttctctatccaatagctacctctggtaacataatttccatccgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGGATGTGGGTGGGCAAGAAAAACTCAGGTCACTGTGGAAGATGTACCTGAG
       |||    || |    |      | |||   |||  ||    | | || |  |  |||  ||  |||  ||   ||| |  ||     | |   ||||||||||||| || |||||||||||||| |||||||||| ||| |||||||||||||| || || |||||||| |||||| || | |||||||||||||| ||
aattatataattctatacctcataattcattgatgtgctcgacttt--ttcccaatcattgatctcatgtctatatccaataataccat----gtaccctctgcagGTTTTAACGTAGAGAAGGTTCAGTACAAGAATGTGGTATTTACTGTGTGGGATGTTGGCGGACAAGAAAAGCTCAGGCCATTATGGAAGATGTACCTCAG

upper sequence: GRMZM2G152929_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ08154 (Selaginella moellendorffii), 3'ss of exon 2
gcctaacataatgctctggcgtctggattgactctgctgcaatcctcatttctctatccaatagctacctctggtaacataatttccatccgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGGATGTGGGTGGGCAAGAAAAACTCAGGTCACTGTGGAAGATGTACCTGAG
                            | |  ||  |    |  |   ||  || ||   | |       || |    | || |  |||| | ||  ||| ||||| || |||||||| ||||| ||||||||||  ||||| ||||||||||||||||| || || || || ||  | || ||||||   ||| | ||
---------------------------gtaatcctttttttctggtttcttggctttcatcttggccttcttgctcgactgatgtgaatccttgct--agGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTGGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG

upper sequence: GRMZM2G152929_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
gcctaacataatgctctggcgtctggattgactctgctgcaatcctcatttctctatccaatagctacctctggtaacataatttccatccgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGGATGTGGGTGGGCAAGAAAAACTCAGGTCACTGTGGAAGATGTACCTGAG
        |||| || |    ||||| ||  ||  |||   ||| | |  |   |   | ||      |||   | |  | |     |||| | ||  ||| ||||| || |||||||| ||||| ||||||||||  ||||| ||||||||||| ||||| || || || || ||  | || ||||||   ||| | ||
-------gtaatccttt--tttctggttt--cttggctttcatcttgaccttcttgctcgatt----tctcgactgatgtga-----atccttgct--agGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG

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|211167703|gb|FL265640.1|FL265640
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCA
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCA
EST: gi|211167696|gb|FL265633.1|FL265633
EST:     ACTGTACAGGCTTCACWTGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|37418653|gb|CF646998.1|CF646998
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|211167701|gb|FL265638.1|FL265638
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTG
EST: gi|211167698|gb|FL265635.1|FL265635
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTT-AATGTCGAGAAGGT-CAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|211167700|gb|FL265637.1|FL265637
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGA
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGA
EST: gi|211169374|gb|FL265646.1|FL265646
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|211166026|gb|FL265625.1|FL265625
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|211169372|gb|FL265644.1|FL265644
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGC
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGC
EST: gi|211166027|gb|FL265626.1|FL265626
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|15427296|gb|BI543118.1|BI543118
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|24766993|gb|CA402138.1|CA402138
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|91875634|gb|EB405591.1|EB405591
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|211167694|gb|FL265631.1|FL265631
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|211166025|gb|FL265624.1|FL265624
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|211167702|gb|FL265639.1|FL265639
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAT-AATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|91875499|gb|EB405456.1|EB405456
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|211503062|gb|FK990412.1|FK990412
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGG
EST: gi|211166029|gb|FL265628.1|FL265628
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|211167692|gb|FL265629.1|FL265629
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|211167693|gb|FL265630.1|FL265630
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|211166024|gb|FL265623.1|FL265623
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|211167697|gb|FL265634.1|FL265634
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
EST: gi|89763974|gb|DY690946.1|DY690946
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAAAAGGTTCAGTATAAAAATGTGGCATTCACTGT
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGT
EST: gi|211166023|gb|FL265622.1|FL265622
EST:     ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCG                         GTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG
genomic: ACTGTACAGGCTTCACATGGGAGAGGTTCTTTCAACAGTCCCTACAGTCGgtaggtggcc ... cgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttctctatccaatagctacctctggtaacataatttccatccgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGGATGTGGGTGGGCAAGAAAAACTCAGGTCACTGTGGAAGATGTACCTGAG
                          tggtaac  putative branch site (score: 2)
                                     tttccatccgtcct  putative PPT
                             taacataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcctaacataatgctctggcgtctggattgactctgctgcaatcctcatttctctatccaatagctacctctggtaacataatttccatccgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGGATGTGGGTGGGCAAGAAAAACTCAGGTCACTGTGGAAGATGTACCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG