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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagtccaatgtctatgcttgctgaaatatttatgtccatattactagtgtatgtacctctcatttgttttctttgaacatttcagGTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTACGCTTGTAATCGCTATGAATCAGCAAAGAAGGAGGGAGTT

Basic information

species Oryza sativa
transcript LOC_Os08g42740.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42740.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G100913_T02 (Zea mays), 3'ss of exon 8
gtatagtccaatgtctatgcttgctgaaatatttatgtccatattactagtgtatgtacctctcatttgtt-ttctttgaacatttcagGTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTACGCTTGTAATCGCTATGAATCAGCAAAGAAGGAGGGAGTT
|||| || || |     | ||   ||||| | ||       | |  |  || ||| | | | |   |||   ||||||| ||||| |||||||||||||||| ||||| | || || || |||||||| ||||| ||||| ||||| ||||| ||||||||||||||||| |||||||||
gtattgttcact-----tactgcttgaaagaattgcagtattctgccatgtttatcttcttttgtcttgaggttctttgcacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTATGCTTGCAATCGTTATGAATCAGCAAAGAAAGAGGGAGTT
















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|29635023|gb|CB640032.1|CB640032
EST:     GAAGGGTATTCTTCTGATGTGATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAG
genomic: GAAGGGTATTCTTCTGATGTGATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAG
EST: gi|29643283|gb|CB648290.1|CB648290
EST:     GGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTG                         GTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTA
genomic: GGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTGgtatagtcca ... aacatttcagGTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTA
EST: gi|29671896|gb|CB668171.1|CB668171
EST:     TTGTGGAATATGTTTTGAAGGGTATTCTTCTGATGTGATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAG
genomic: TTGTGGAATATGTTTTGAAGGGTATTCTTCTGATGTGATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAG
EST: gi|29643281|gb|CB648288.1|CB648288
EST:     GGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTG                         GTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTA
genomic: GGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTGgtatagtcca ... aacatttcagGTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTA
EST: gi|29677672|gb|CB673947.1|CB673947
EST:     GGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTG                         GTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTA
genomic: GGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTGgtatagtcca ... aacatttcagGTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtccatattactagtgtatgtacctctcatttgttttctttgaacatttcagGTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTACGCTTGTAATCGCTATGAATCAGCAAAGAAGGAGGGAGTT
       atattacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagtccaatgtctatgcttgctgaaatatttatgtccatattactagtgtatgtacctctcatttgttttctttgaacatttcagGTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTACGCTTGTAATCGCTATGAATCAGCAAAGAAGGAGGGAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG