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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caggtgtgcagccaaacaagccttcagggttattattccaaagtgactaccatgttatacttcagattgtggtgattatgtaattatatatttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGACCTTTTTGTTTGTTACCGATCAGAAGAGGATCTGGAGGTTGCCCCTTTC

Basic information

species Zea mays
transcript GRMZM2G099547_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099547_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g19470.1 (Oryza sativa), 3'ss of exon 2
---cag-gtgtgcagc-caaacaagcctt--cagggttattatt-ccaaagtgactaccatgttatacttcagattgtggtgattatgtaattatatatttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGACCTTTTTGTTTGTTACCGATCAGAAGAGGATCTGGAGGTTGCCCCTTTC
   ||   | | ||   |  | | ||| |  | || | ||| |    ||  | | ||| | |||  ||| || | | || ||||| | ||||          |||||| || ||||| ||||||||||||||||| || ||||| ||| ||||||| | |||||| |||||||||||||||||||||||  ||||| | || || |||
catcaccatttacaattcttatatgccatatctggatcattttggttaatataattactaggttgcactccaaactttgatgattctctaatg--------tatgcagGGGAGAAGGGAAGCTTGAAAAGCAGTTCCGTATGAGTTGTTTGGGATGCGGCCTTTTCGTTTGTTACCGATCAGAAGAGGAGTTGGAGCTAGCTCCATTC
















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|211360254|gb|FL253403.1|FL253403
EST:     CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|78117103|gb|DV535490.1|DV535490
EST:     CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|211360251|gb|FL253400.1|FL253400
EST:     CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|32788063|gb|CD940299.1|CD940299
EST:     TAAGGAGGCAGGAAAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: TAAGGAGGCAGGAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|60394679|gb|DN227549.1|DN227549
EST:     GCAGGAAAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: GCAGGAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|211357595|gb|FL253396.1|FL253396
EST:     CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAASSAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|78075508|gb|DV503942.1|DV503942
EST:     CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|60348216|gb|DN215189.1|DN215189
EST:     AAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: AAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|86471527|gb|DY237897.1|DY237897
EST:     GGCAGGAAAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: GGCAGGAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|60337543|gb|DN204516.1|DN204516
EST:     GCAGGAAAAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: GCAGG-AAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|71433975|gb|DR815025.1|DR815025
EST:     CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|148980593|gb|EE027217.2|EE027217
EST:     CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|149104413|gb|EE289858.2|EE289858
EST:     CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|50325142|gb|CO520268.1|CO520268
EST:     CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|84351516|gb|DW245921.1|DW245921
EST:     TCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: TCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|16925502|gb|BM078570.1|BM078570
EST:     AAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: AAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|211360248|gb|FL253397.1|FL253397
EST:     CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACG                         TTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTG
genomic: CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagT-GGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTG
EST: gi|78180203|gb|DV550576.1|DV550576
EST:     AATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: AATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|6827273|gb|AW330916.1|AW330916
EST:     GAAAAGTAATGTTGAAACG                         TGG-GAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: GAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
EST: gi|71450211|gb|DR831261.1|DR831261
EST:     CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACG                         TGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA
genomic: CATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAACGgtataataat ... tttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actaccatgttatacttcagattgtggtgattatgtaattatatatttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGACCTTTTTGTTTGTTACCGATCAGAAGAGGATCTGGAGGTTGCCCCTTTC
                           tgattatgtaattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caggtgtgcagccaaacaagccttcagggttattattccaaagtgactaccatgttatacttcagattgtggtgattatgtaattatatatttcatgcagTGGTGAAGGAAAGCTTGAAAAGCAGTTTCGCATGAGCTGTGTGGGATGTGACCTTTTTGTTTGTTACCGATCAGAAGAGGATCTGGAGGTTGCCCCTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG