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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttctcttcatctgtagtattttatcattgtggctttgaaaaatcaaatatcatttgaacacaacatgattttgtttctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG

Basic information

species Zea mays
transcript GRMZM2G102639_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102639_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g31900.1 (Oryza sativa), 3'ss of exon 4
----gtattttctcttcatctgtagt-attttatcattgtggctttgaaaaatcaaatatcatttgaacac---aacatgatt-ttgtttctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG
     || |   |||  | || |  | ||| ||||        || |||| ||   || | | |   |||    ||||||||| |  |||||| ||||||||||| || || ||||||||| | || || || |||||||| |||||||||||||| ||||||
cagtatactgcttctaaaactttctttattatatctaaacattttcgaaatataggatttaaatatcacatggtaacatgattatcttttcttattccagGCTTCACAAGACAAGAAGAGCCTTGATGTAGGGGCAAATCTTTTTATTGGCAATCTCGATCCG

upper sequence: GRMZM2G102639_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G36950.1 (Glycine max), 3'ss of exon 4
gtattttctcttcatct-gtagtattt-tatcattgtggctttgaaaaatcaaatatc--atttgaacacaacatgat------tttgtttcttt--ttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG
     || |  | || | || ||||    | | ||||  ||| ||  ||  ||| ||    |||  |  |    ||||      | || || |||  ||| |||| ||||| ||||| |||||| |||| ||||| |||||||| || ||||||||||||||||| 
--tccttgtagtaatgtagttgtatcaacacccttgtcactt-gattaacaaaacatttagttttcatgctgtttgatggattttatgattttttggttctagGCATCCCAAGATAAAAAGAGCCTGGATGTTGGTGCAAATCTTTTCATTGGCAATCTTGATCCT

upper sequence: GRMZM2G102639_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G00310.1 (Glycine max), 3'ss of exon 4
------gtattttctcttcatctgtagtattttatcattgtggctttgaaaaatcaaatatcatttgaacacaacatgattttg----tttctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG
       |||||  || |  | |  |      |  || |         ||| ||  | | ||  |    |   |  |||||||     ||| |  |||||||| ||||| ||||| ||||||||||| ||||| |||||||| || ||||||||||| ||||| 
cctgctatatttcttccttgtattaacacccatgccacttgattaacaaaatatttagtttctatgctgcttgat-tgattttacaattttttggttccagGCATCCCAAGATAAAAAGAGCTTGGATGTTGGGGCAAATCTTTTCATTGGCAATCTAGATCCT

upper sequence: GRMZM2G102639_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------------gtattttctct-----tcatctgtagtattttatcattgtggctttgaaaaatcaaatatcatttgaacaca-------acatgattttgtttcttttt----------ccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG
                                               ||  ||| ||      | |  | |    | |  | ||  | | || ||     || | ||  ||  || | |         ||||| || || |  |||          |||||| || || ||||| ||||||||||| ||||||||||| || ||| |||| || |||||||| 
gtgtgacatttattttcactagctatctcatttgccttatttcttatgttctttttcagactatgagttatgaagtgtagttatatttgtttggagcgtccataaattcttataaaatatgtgtttgtatgatctttttccccttttttattggttccagGCATCTCAAGATAAAAAGAGCTTGGATGTTGGAGCAAACCTTTTTGTTGGAAACCTTGATCCT

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|26558877|gb|CA831112.1|CA831112
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|78090866|gb|DV519240.1|DV519240
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|91056510|gb|EB166928.1|EB166928
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|148943004|gb|EC888052.2|EC888052
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|87157489|gb|DY402278.1|DY402278
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|33467168|gb|CF244217.1|CF244217
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|148956981|gb|EC902927.2|EC902927
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|148933043|gb|EE285938.2|EE285938
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|78124664|gb|DV543048.1|DV543048
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGAAAACAAG                         GCTTCCCAGGATAAAAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|50322326|gb|CO517452.1|CO517452
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|89762379|gb|DY689990.1|DY689990
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|94477767|gb|EB706725.1|EB706725
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|76288123|gb|DV027691.1|DV027691
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|71425499|gb|DR806709.1|DR806709
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|31355533|gb|CD439890.1|CD439890
EST:     GACTTTGAACATGATCAAACTAT-TCGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: GACTTTGAACATGATCAAACTATAT-GGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|76291455|gb|DV031023.1|DV031023
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|76015742|gb|DT942912.1|DT942912
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|76290093|gb|DV029661.1|DV029661
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|148961210|gb|EE011925.2|EE011925
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTTGGAGCAAATCCTGTTTATTG
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTT-GGAGCAAATC-TGTTTATTG
EST: gi|86472905|gb|DY239275.1|DY239275
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAGG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|78124734|gb|DV543118.1|DV543118
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAAAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|148938096|gb|EC882358.2|EC882358
EST:     AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGACTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttctc ... ctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttgaaaaatcaaatatcatttgaacacaacatgattttgtttctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG
                                     ttttgtttctttttcc  CT-rich tract
      aaaaatcaaatatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttctcttcatctgtagtattttatcattgtggctttgaaaaatcaaatatcatttgaacacaacatgattttgtttctttttccagGCTTCCCAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA