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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatacggtgtttggaatatgcctatgatctttgttccatttgtttatacataaatgtttacaatttgttgcttatcttatgacacaattttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAAT

Basic information

species Oryza sativa
transcript LOC_Os03g25940.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g25940.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G075153_T02 (Zea mays), 3'ss of exon 4
gaata-cggtgtttggaatatgcctatgatctttgttccatttgtttatacataaatgtttacaatttgttgcttatcttatgacacaattttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAAT
 |||| |     ||| |||      |      ||  |   |||   |||| |  ||||||||  ||   |  ||||     ||   |  ||| ||||| ||||||| || ||||| |||||||||||||||||||||||||||||  |||| || ||||||
caatatctagagttgaaatgcagtgagagcactttgtaagttttgctatataccaatgtttatcatgcttcacttagtacgtggtgctgttt-gtgtctagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTCCAAAATGCGTTGGACAACAATAAT

upper sequence: LOC_Os03g25940.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G113873_T02 (Zea mays), 3'ss of exon 4
gaatacggtgtttggaatatgcctatgatctttgttccatttgt---ttatacataaatgtttacaatttgttgcttatcttatgacacaattttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAAT
 |  ||    | |   |  ||   |||   |  |  |  |||||   || || |  |||||||   |    |  |||| | | ||| ||  |||  ||  |||||||| || ||||| |||||||||||||||||||| ||||||||  |||| || ||||||
-atcacaccatctaccagttgaa-atgcagtgagagcactttgtgagttgtataccaatgtttctcacgcttcacttagcatgtgatactgttt-atgctcagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGACAACAATAAT
















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|58694049|gb|CK082736.1|CK082736
EST:     GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACG                         ATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
genomic: GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACGgtaatctgat ... ttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
EST: gi|29625314|gb|CB630325.1|CB630325
EST:     GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTATG                         ATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
genomic: GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACGgtaatctgat ... ttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
EST: gi|29614913|gb|CB619926.1|CB619926
EST:     GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACG                         ATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
genomic: GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACGgtaatctgat ... ttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
EST: gi|38478380|gb|CF962513.1|CF962513
EST:     GCAAGACGAGAATTTACATGGAGACTGAACTACCTAGGAGGGGAATTACG                         ATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
genomic: GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACGgtaatctgat ... ttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
EST: gi|58612841|gb|CK040553.1|CK040553
EST:     GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACG                         ATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAGAGTGCACTGGA
genomic: GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACGgtaatctgat ... ttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAA-AATGCACTGGA
EST: gi|112785728|gb|EE591291.1|EE591291
EST:     GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACG                         ATGACCGTTATTAGACCTGCCGACATGGATGC-CACCAAAA
genomic: GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACGgtaatctgat ... ttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAA
EST: gi|58695584|gb|CK084271.1|CK084271
EST:     GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACG                         ATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
genomic: GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACGgtaatctgat ... ttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
EST: gi|29645224|gb|CB650231.1|CB650231
EST:     GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACG                         ATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
genomic: GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACGgtaatctgat ... ttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
EST: gi|58658021|gb|CK046701.1|CK046701
EST:     GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACG                         ATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
genomic: GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACGgtaatctgat ... ttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
EST: gi|58596991|gb|CK007519.1|CK007519
EST:     GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACG                         ATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
genomic: GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACGgtaatctgat ... ttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
EST: gi|55411461|gb|CV723837.1|CV723837
EST:     GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACG                         ATGACCGTTAT
genomic: GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACGgtaatctgat ... ttgtgtccagATGACCGTTAT
EST: gi|58612205|gb|CK039917.1|CK039917
EST:     GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACG                         ATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
genomic: GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACGgtaatctgat ... ttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
EST: gi|29614165|gb|CB619178.1|CB619178
EST:     GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACG                         ATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
genomic: GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACGgtaatctgat ... ttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
EST: gi|218484474|gb|FG954293.1|FG954293
EST:     GCAAGACGAGAA-TTACATGGAGACTGAACTACCTAAGAGGGGAATTACG                         ATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
genomic: GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACGgtaatctgat ... ttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
EST: gi|29660676|gb|CB656951.1|CB656951
EST:     GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACG                         ATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT
genomic: GCAAGACGAGAATTTACATGGAGACTGAACTACCTAAGAGGGGAATTACGgtaatctgat ... ttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacataaatgtttacaatttgttgcttatcttatgacacaattttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAAT
     ataaatgtttacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatacggtgtttggaatatgcctatgatctttgttccatttgtttatacataaatgtttacaatttgttgcttatcttatgacacaattttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA