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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttggtgtttagtgctcatagctcaggacatgcttctaatatcgcaaaagctttttcatgcatgcttgtaccatgggcatttccccaatcttgcag

Basic information

species Zea mays
transcript GRMZM2G140689_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140689_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os06g06410.1 (Oryza sativa), 5'ss of exon 7
CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttggtgtttagtgctcatagctcaggacatgcttctaatatcgcaaaagctttttcatgcatgcttgtaccatgggcatttccccaatcttgcag
||||| |||||||| || || || ||||||||||||||||||||||||||||||||||||  |||       ||  || | |||               || || |||  ||| ||    |  |||||  |  ||||    | | | |||| | | ||
CACAAGTGCTACATCGTCGCAACATGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtacattta----caagcactta-agcctg------------aacattgcagcagccttgctct-tatgctaattacatgtttgtgttctcaatttggtag

upper sequence: GRMZM2G140689_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT1G26530.1 (Arabidopsis thaliana), 5'ss of exon 7
CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttggt-gtttagtgctcatagctcaggacatgcttctaatatcgcaaaagctttttcatgcatgcttgtaccatgggcatttccccaatcttgcag
|| ||||||| |||||| |||||||||||||||||| | ||  | |||||  | ||||||    || | ||||  |    ||   |   || || |       || || |      ||  |||    |||      ||  | |||              
CATAAATGCTTCATAGTAGCTACTTGTGATAGAGATCTAAAGCGAAGGATTCGCAAGgtaaagatgttagtttgatatatatgctttttgaaatcc-------atggctaggatccttggatgttaactttcttattgttcgtttatag----------
















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:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|71445647|gb|DR826697.1|DR826697
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|88754303|gb|DY538444.1|DY538444
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|89252677|gb|DY624463.1|DY624463
EST:     ATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCGTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: ATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|93013575|gb|EB639095.1|EB639095
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|88746998|gb|DY531139.1|DY531139
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|74236372|gb|DT644286.1|DT644286
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|76021687|gb|DT948857.1|DT948857
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|19770099|gb|BQ034820.1|BQ034820
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|50326783|gb|CO521909.1|CO521909
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|74245266|gb|DT653180.1|DT653180
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|211295565|gb|FL447041.1|FL447041
EST:     GCTATATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|50332974|gb|CO528100.1|CO528100
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|89247134|gb|DY618920.1|DY618920
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|211091999|gb|FL476412.1|FL476412
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|93011681|gb|EB637201.1|EB637201
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|166471289|gb|EG109651.1|EG109651
EST:     CTTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGA
genomic: C-TACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGA
EST: gi|74239821|gb|DT647735.1|DT647735
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|213173441|gb|FM193835.1|FM193835
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|76018425|gb|DT945595.1|DT945595
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|19769624|gb|BQ034345.1|BQ034345
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|50326824|gb|CO521950.1|CO521950
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|78025632|gb|DV494019.1|DV494019
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|33468200|gb|CF245249.1|CF245249
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|78077064|gb|DV505498.1|DV505498
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|50330326|gb|CO525452.1|CO525452
EST:     TGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: TGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|76292363|gb|DV031931.1|DV031931
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|5688786|gb|AI941801.1|AI941801
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|5649962|gb|AI920322.1|AI920322
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttggtgtttagtgctcatagctcaggacatgcttctaatatcgcaaaagctttttcatgcatgcttgtaccatgggcatttccccaatcttgcag

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