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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaagtacacagatcacaatttttgtgttatttgttcgacgttctttccattgattgaatgttgtaaggatggtggataactgtaagtcatatctggtgttgcctgacag

Basic information

species Zea mays
transcript GRMZM2G095252_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g02380.2 (Oryza sativa), 5'ss of exon 9
GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtat--tgtgaagtacacagatcacaatttttgtgttatttgttcgacgttctt-tccattgattg-aatgttgtaaggatggtggata-----actgtaagtcatatctggtgttgcctgacag
|| || ||||||||||| || ||||||||||||||||||||||| ||||||||||||||||||||||| |||||||||||||  |  ||| |  ||| |   | || ||     ||| |||||    |  |  | | ||| ||| || | |  |  |||| ||| ||        ||||  ||  | | ||      ||| ||
GCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAGCTTGCTGGTGGTGTTGCAGTCATTCAGgtataataagaaatggacaaaatgccatgttatctgtatctgttctttttcttggttctttgtttggaaagatagatagatg-tggttatgtgggtcgtaatccaagttttgttacttttgatag

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 9
GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaagtacacagatcacaatttttgtgttatttgttcgacgttctttccattgattgaatgttgtaaggatggtggataactgtaagtcatatctggtgttgcctgacag
  ||| || ||||| || || ||||| || ||||||||||| || ||||||||  ||||||| |||||||| |||||||||     || || | |      || |||  | || | || |  |  |   || ||  |||   | |||       |  || ||   |  |||                       
CAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAGgta-----aactaaaaactatttaagtttcct-ttgtctgattaagatgtgtttcagagatattaagttaagctcgttatgtattggttaaag-----------------------

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 5'ss of exon 9
GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtga-agtacacagatcacaatttttgtgttatttgttcgacgttctttccattgattgaatgttgtaaggatggtggataactgtaagtcatatctggtgttgcctgacag
|| || |||||||| ||||||||||||||||| |||||||| || || ||  |  | || ||||||||||| ||||||||    |   |  | ||| ||||||    |  ||  |   |     | ||      ||     ||||  | |||  | | |  |||    | ||                       
GCTGCTGAACAAGACTATGAAAAGGAAAAGCTTAATGAGAGAATTGCTAAATTATCAGGCGGTGTTGCTGTAATTCAGgtgagatactaagaaacaaatcaca----tgatgcaaaaagcgtagc-ttaaggtaataagaagaataatctaa--acgttttatattctttag-----------------------

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 9
GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgta--ttgtgaagtacacagatcacaatttttgtgttatttgttcg----acgttctttccattgattgaatgttgtaaggatggtggataactgtaagtcatatctggtgttgcctgacag
|||||||| ||||||||||| |||||||| || ||||| || || |||||  |  | |||||||||||||| |||||||||  || | |  ||  |   | | ||||| |   | ||||  ||     | || |||   ||  ||| | | ||    | |   | ||                                 
GCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGgtaaattcttagttagtccagttaaaatttataaatgatttcatcattgcaggtgcttagtatctattaattattcattgaacttttgaag-------------------------------

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 8
GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgta-ttgtgaagtacacagatcacaatttttgtgttatttgttcgacgttctttccattgattgaatgttgtaaggatggtggataactgtaagtcatatctggtgttgcctgacag
|||||||| || || |||||||| || ||||| ||||| || || ||||| ||| | |||||||||||||||||||||||| || |    |      |  ||||| |   ||||  ||| | || |   ||   |  |  |   | || |           |  | | ||| |  | | | |      | |    
GCAGCAGATCAGGACTATGAAAAAGAGAAGCTTAATGAAAGAATTGCAAAACTTTCAGGTGGTGTTGCTGTCATTCAGgtaatttttttttttcttaaatacaatgtagctgttggttgatagatggaattctgaaagtattgttctttt-----ctacccactattttaatttttgtgttgcacattcag----

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|32837509|gb|CD977187.1|CD977187
EST:     AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaa ... tgcctgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
EST: gi|32932965|gb|CF037777.1|CF037777
EST:     AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGGAGAAGTTAAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaa ... tgcctgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
EST: gi|33092673|gb|CF052667.1|CF052667
EST:     AGCTCAATGAGGGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaa ... tgcctgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
EST: gi|32934171|gb|CF038983.1|CF038983
EST:     AGCTCAATGAGCGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaa ... tgcctgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
EST: gi|211046936|gb|FL343169.1|FL343169
EST:     AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACT
genomic: AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaa ... tgcctgacagGTGGGAGCACAAACAGAAACTGAACT
EST: gi|32931699|gb|CF036511.1|CF036511
EST:     AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaa ... tgcctgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
EST: gi|32935108|gb|CF039920.1|CF039920
EST:     AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaa ... tgcctgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
EST: gi|32931097|gb|CF035909.1|CF035909
EST:     AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaa ... tgcctgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
EST: gi|32836365|gb|CD976043.1|CD976043
EST:     AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaa ... tgcctgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
EST: gi|32935122|gb|CF039934.1|CF039934
EST:     AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaa ... tgcctgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
EST: gi|32838764|gb|CD978445.1|CD978445
EST:     AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaa ... tgcctgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
EST: gi|211173892|gb|FL341459.1|FL341459
EST:     AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGKGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAARAGTTGAG
genomic: AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaa ... tgcctgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
EST: gi|32930569|gb|CF035381.1|CF035381
EST:     AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGCTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaa ... tgcctgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
EST: gi|33097092|gb|CF057052.1|CF057052
EST:     AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAG                         GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG
genomic: AGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaa ... tgcctgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAGgtattgtgaagtacacagatcacaatttttgtgttatttgttcgacgttctttccattgattgaatgttgtaaggatggtggataactgtaagtcatatctggtgttgcctgacag

- - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG