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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcctttgtgatcaaaacttgaaaccacaatatgaactcacatgttatccaatgtgccctgtttttttgtcaaaccgtgtgtttacgaattcttg...

Basic information

species Zea mays
transcript GRMZM2G169773_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169773_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g57220.2 (Oryza sativa), 5'ss of exon 3
GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcctt-tgtgatcaaaacttgaaaccacaatatgaactcacatgttatccaatgtgccctgtttttttgtcaaaccgtgtgtttacgaattcttg
||| | |  ||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||| |||  | |    |  ||     ||| |  | |   || || ||    |     || |||||   |||    ||        ||    | 
GACATGAAGAAAAAGGAGAAAGAACTGCAGGCAAAGGAGGCTGAGCTAAACAAACGGGAAAGCgtatgtgccttctgtagttatgcttgaaacttggaattttcaattg-atcttttcatgagcaatgtgatttttaaccaatgtttgatgaagtaaaaaacta
















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|148980186|gb|EE026996.2|EE026996
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
EST: gi|211370168|gb|FL333601.1|FL333601
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
EST: gi|211265380|gb|FL345555.1|FL345555
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
EST: gi|211534447|gb|FL327599.1|FL327599
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCCAGAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCC-AGAG
EST: gi|71449251|gb|DR830301.1|DR830301
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
EST: gi|211525880|gb|FL340827.1|FL340827
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
EST: gi|211278417|gb|FL366616.1|FL366616
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTG
EST: gi|211425017|gb|FL340245.1|FL340245
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
EST: gi|211196276|gb|FL364468.1|FL364468
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
EST: gi|211433369|gb|FL360626.1|FL360626
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAG
EST: gi|78077114|gb|DV505548.1|DV505548
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
EST: gi|211015839|gb|FL346618.1|FL346618
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGCTG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGCTG
EST: gi|211537608|gb|FL330675.1|FL330675
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
EST: gi|211231053|gb|FL343819.1|FL343819
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
EST: gi|78115059|gb|DV533447.1|DV533447
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
EST: gi|211012583|gb|FL327130.1|FL327130
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
EST: gi|211067503|gb|FL350735.1|FL350735
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
EST: gi|71429331|gb|DR810381.1|DR810381
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
EST: gi|211146797|gb|FL347631.1|FL347631
EST:     AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG                         GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG
genomic: AGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcct ... tgaccctcagGAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGGgtatgtgcctttgtgatcaaaacttgaaaccacaatatgaactcacatgttatccaatgtgccctgtttttttgtcaaaccgtgtgtttacgaattcttg

- - - - - -  AGGAGA
- - - - - - - GGAGAA
- - - - - - - - - AAAGAA
- - - - - - - - -  AAGAAC
- - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - AGCTGA