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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCACTTGTCCCTGCTGGTGGGCACATTGTGACCACCACGGATTGCTACCGCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgtgctatcctttaagctcaacttgtttttggaacgggatatctgctagattaaccgtcttcctgtcactgtgttacagtagtgcttttacag...

Basic information

species Zea mays
transcript GRMZM2G075153_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075153_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g25940.4 (Oryza sativa), 5'ss of exon 5
CGCACTTGTCCCTGCTGGTGGGCACATTGTGACCACCACGGATTGCTACCGCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgtgctatcctttaagctcaacttgtttttggaacgggatatctgctagattaaccgtcttcctgtcactgtg--ttacagtagtgcttttacag--
||| ||||| || || ||||||||| ||||||||||||| ||||| ||||||||||| || ||||||||||| | ||| || ||||||||||||||| |||||||    |  |||  ||   | |      ||  |    | |  |  |    | || |     ||||   ||   ||||  ||    | || || |   ||  
CGCGCTTGTTCCAGCAGGTGGGCACGTTGTGACCACCACTGATTGTTACCGCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACGgtaatctgatcttattattcttgtttg--cagtaatgcatatgtaactttcaatggagt--ttttcttgtagttgatgtgacttgtcattgttctatagtagca

upper sequence: GRMZM2G075153_T02 (Zea mays), 5'ss of exon 4
lower sequence: EFJ15929 (Selaginella moellendorffii), 5'ss of exon 4
CGCACTTGTCCCTGCTGGTGGGCACATTGTGACCACCACGGATTGCTACCGCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgtgctatcctttaagctcaacttgtttttggaacgggatatctgctagattaaccgtcttcctgtcactgtgttacagtagtgcttttacag
 ||  | || ||||||||||| |||||||| ||||| || ||||||||||| |  ||||||   | | |  | | || |||||| || | ||| ||  ||||| | |||   | |||  |  |  ||| || |  ||    ||| ||   | | | | |     |||| | |                            
GGCTTTGGTTCCTGCTGGTGGACACATTGTAACCACGACTGATTGCTACCGTAGAACAAGGCAGTTCGTCCAGACTGTGCTCCCCAAAATGGGGATAACGgta-tgctgatttctcccgttcg--caagttttccttctctcggtatcgattc-atacttgttatctttcag----------------------------
















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|211234235|gb|FL407898.1|FL407898
EST:     GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
genomic: GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgt ... ttgtgtctagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
EST: gi|30705385|gb|CD058765.1|CD058765
EST:     GCAAGACAAGGATTTACATGGAA--TGAGCTCCCTAAGAGGG-AATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCT
genomic: GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgt ... ttgtgtctagATGACTGTCATTAGGCCTGCTGACATGGATGCT
EST: gi|30705650|gb|CD058859.1|CD058859
EST:     GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
genomic: GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgt ... ttgtgtctagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
EST: gi|211303407|gb|FL181618.1|FL181618
EST:     TCCCTAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
genomic: TCCCTAAGAGGGGAATTTCGgtaatactgt ... ttgtgtctagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
EST: gi|61119178|gb|DN560139.1|DN560139
EST:     GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
genomic: GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgt ... ttgtgtctagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
EST: gi|5343071|gb|AI795481.1|AI795481
EST:     AGGA-TTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
genomic: AGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgt ... ttgtgtctagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
EST: gi|22133730|gb|BQ833872.1|BQ833872
EST:     GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
genomic: GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgt ... ttgtgtctagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
EST: gi|29946125|gb|CB815991.1|CB815991
EST:     GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
genomic: GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgt ... ttgtgtctagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
EST: gi|149074757|gb|EE163186.2|EE163186
EST:     GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
genomic: GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgt ... ttgtgtctagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
EST: gi|149108488|gb|EE189677.2|EE189677
EST:     GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
genomic: GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgt ... ttgtgtctagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
EST: gi|148948278|gb|EC893795.2|EC893795
EST:     GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
genomic: GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgt ... ttgtgtctagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
EST: gi|38229609|gb|CF919922.1|CF919922
EST:     GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
genomic: GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgt ... ttgtgtctagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
EST: gi|211066604|gb|FL423906.1|FL423906
EST:     GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCG                         ATTGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGA
genomic: GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgt ... ttgtgtctagAT-GACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGA
EST: gi|91873684|gb|EB403641.1|EB403641
EST:     GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC
genomic: GCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgt ... ttgtgtctagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCACTTGTCCCTGCTGGTGGGCACATTGTGACCACCACGGATTGCTACCGCAAGACAAGGATTTACATGGAAAATGAGCTCCCTAAGAGGGGAATTTCGgtaatactgtgctatcctttaagctcaacttgtttttggaacgggatatctgctagattaaccgtcttcctgtcactgtgttacagtagtgcttttacag

- - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG