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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctacggcatcttgttttattttgtttctaaaccataaaattttacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG

Basic information

species Zea mays
transcript GRMZM2G140689_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140689_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g06410.1 (Oryza sativa), 3'ss of exon 6
-----nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctacggcatcttgttttattttgtttctaaaccataaaattttacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG
                                                      ||    || | | |  ||||||   ||||||   ||  ||||  ||  |||||||| |||||||| || || || |||||||||||||||||||||||||||||||||
gaaagtttaagactagtttttgtgataatcatttggatctatgtagcttgtgtgtaaaaaatttcgcta-attttg---ctaaactgcaac-ttttctgtaacagCACAAGTGCTACATCGTCGCAACATGTGATAGAGATTTGAAAAGGAGGATAAGAAAG

upper sequence: GRMZM2G140689_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G26530.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctacggcatcttgttttattttgtttctaaaccataaaattttacgtgg-cagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG
                                                              |   |||| | || | || || | | |    | |     | ||  |   ||||| ||||||| |||||| |||||||||||||||||| | ||  | |||||  | |||
gtaatgcctcagctccggttttgtttaccatcgtgtcttgtttctctaagaagatgctctgtttatgcatgtagtctaatcttctgtttgtttctttcctctgtaattaatcagCATAAATGCTTCATAGTAGCTACTTGTGATAGAGATCTAAAGCGAAGGATTCGCAAG
















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|31352269|gb|CD436626.1|CD436626
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|71445647|gb|DR826697.1|DR826697
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|88754303|gb|DY538444.1|DY538444
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|93013575|gb|EB639095.1|EB639095
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|88746998|gb|DY531139.1|DY531139
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|74236372|gb|DT644286.1|DT644286
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|76021687|gb|DT948857.1|DT948857
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|19770099|gb|BQ034820.1|BQ034820
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTG-GGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|50326783|gb|CO521909.1|CO521909
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|74245266|gb|DT653180.1|DT653180
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|211295565|gb|FL447041.1|FL447041
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTATATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|50332974|gb|CO528100.1|CO528100
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|89247134|gb|DY618920.1|DY618920
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|211091999|gb|FL476412.1|FL476412
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|93011681|gb|EB637201.1|EB637201
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|74239821|gb|DT647735.1|DT647735
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|213173441|gb|FM193835.1|FM193835
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|76018425|gb|DT945595.1|DT945595
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|19769624|gb|BQ034345.1|BQ034345
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|50326824|gb|CO521950.1|CO521950
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|78025632|gb|DV494019.1|DV494019
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|33468200|gb|CF245249.1|CF245249
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|78077064|gb|DV505498.1|DV505498
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|76292363|gb|DV031931.1|DV031931
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|5688786|gb|AI941801.1|AI941801
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
EST: gi|5649962|gb|AI920322.1|AI920322
EST:     CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG                         CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA
genomic: CACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGgtaaaagctc ... tacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

nnnctacggcatcttgttttattttgtttctaaaccataaaattttacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG
                           ttctaaa  putative branch site (score: 2)
             ttgttttattttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctacggcatcttgttttattttgtttctaaaccataaaattttacgtggcagCACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA