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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatttttaatgttctttactagattcggcgattaatttcatgtattgaatattggcaaaagctatgcatggtgggatgtttaaggaacatcttattgttcataatttatggaaatgattcagtggattcatccatatgatcattttaatctattgtattttctaacttttactttatttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCAAGACATTGCTTACAGGCACTGGTGAAACTATCAGCTACAAAACTCTAAT

Basic information

species Zea mays
transcript GRMZM2G320307_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G320307_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g47790.1 (Oryza sativa), 3'ss of exon 3
gtagatttttaatgttctttactagattcggcgattaatttcatgtattgaatattggcaaaagctatgcatggtgggatgtttaaggaacatcttattgttcataatttatggaaatgattcagtggatt-catccatatgatcattttaatctattgta-ttttctaacttttactttatttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCAAGACATTGCTTACAGGCACTGGTGAAACTATCAGCTACAAAACTCTAAT
                                                                                           || || |||    |  |||     |   ||  |||  ||   || ||   | | || || | |  |  || |  | |   |  |  || | |||| ||||||||| ||||||||||||||| |  |||||||||||||||||| |||  |||||||||||||||  || ||| ||||| |||||||| |||||||| ||
------------------------------------------------------------------------------------------gatatttttgcctcttctttgatctagcaatcaagtcaatcgtattcactagtttatgttcagcactgataatcctgtctatgatctttcacttgactagGCATTGTACTTGTTCTTGGAACGAGGGTGATTTCTGCTGATGTGCGGCAGAAGACATTGCTTACATCCAGTGGGGAAACCATCAGCTATAAAACTCTTAT
















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|78112090|gb|DV530486.1|DV530486
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|13558384|gb|BG549740.1|BG549740
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|211343496|gb|FL158171.1|FL158171
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|148960823|gb|EE011492.2|EE011492
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|74239090|gb|DT647004.1|DT647004
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|76282291|gb|DV021859.1|DV021859
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|211343497|gb|FL158172.1|FL158172
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCAAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|76294433|gb|DV034001.1|DV034001
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|91052072|gb|EB162490.1|EB162490
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTG
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTG
EST: gi|149014462|gb|EE044078.2|EE044078
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|93282877|gb|EB675141.1|EB675141
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|101396936|gb|EB820393.1|EB820393
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|50324177|gb|CO519303.1|CO519303
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|93014386|gb|EB639906.1|EB639906
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|211341114|gb|FL158167.1|FL158167
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTSATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|74236111|gb|DT644025.1|DT644025
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|13198566|gb|BG354385.1|BG354385
EST:     ATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: ATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|148957305|gb|EC903342.2|EC903342
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|87155794|gb|DY400583.1|DY400583
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCAAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|148969919|gb|EE020823.2|EE020823
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|76015963|gb|DT943133.1|DT943133
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|31360581|gb|CD444938.1|CD444938
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|74233733|gb|DT641647.1|DT641647
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|211343502|gb|FL158177.1|FL158177
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTYCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
EST: gi|148949714|gb|EC895192.2|EC895192
EST:     TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAG                         GCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA
genomic: TGTTGGTGCTAATGATGAGTTACTGACACCGAAATGGTACAAAGAACAAGgtagattttt ... atttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatatgatcattttaatctattgtattttctaacttttactttatttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCAAGACATTGCTTACAGGCACTGGTGAAACTATCAGCTACAAAACTCTAAT
                             ttctaac  putative branch site (score: 1)
                                   cttttactttattt  CT-rich tract
           attttaatctattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagatttttaatgttctttactagattcggcgattaatttcatgtattgaatattggcaaaagctatgcatggtgggatgtttaaggaacatcttattgttcataatttatggaaatgattcagtggattcatccatatgatcattttaatctattgtattttctaacttttactttatttgattagGCATTGAACTTGTTCTTGGAACAAAAGTGATTTCTGCTGATGTGAGGCGCAAGACATTGCTTACAGGCACTGGTGAAACTATCAGCTACAAAACTCTAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT