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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggttttgtgctagaagtaatatttcccacacctagtatatgtctgttaatatgatgtgattgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCCTGAAGAGAAATATACGAATGCATTTCTTGGGTTTGGACCTGAGGACACC

Basic information

species Oryza sativa
transcript LOC_Os08g09250.3
intron # 1
splice site 3'
intron type U2

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|38483262|gb|CF967064.1|CF967064
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|428745|gb|D24899.1|D24899
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|7219920|gb|AU063009.2|AU063009
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|58594310|gb|CF992618.1|CF992618
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|88696013|gb|CI739588.1|CI739588
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|58585603|gb|CF983911.1|CF983911
EST:     GGCTTCTACATGCTGTTTACCTGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: GGCTTCTACATGCTGTTTACC-GTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|58688050|gb|CK076737.1|CK076737
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|218493123|gb|FG968720.1|FG968720
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|58601044|gb|CK011572.1|CK011572
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|58682272|gb|CK070959.1|CK070959
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|11025939|gb|AU162540.1|AU162540
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|218504483|gb|FG959632.1|FG959632
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|163921167|gb|EG710156.1|EG710156
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|58676433|gb|CK065120.1|CK065120
EST:     AGGCTTCTACATGCTGTATACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|218502183|gb|FG956191.1|FG956191
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|55828156|gb|AU065471.3|AU065471
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|58591117|gb|CF989425.1|CF989425
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTNGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|58591648|gb|CF989956.1|CF989956
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|58684222|gb|CK072909.1|CK072909
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|58586439|gb|CF984747.1|CF984747
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTGTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
EST: gi|9886121|gb|AU063011.2|AU063011
EST:     AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAA                         ATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC
genomic: AGGCTTCTACATGCTGTTTACCGTGTTGGAGATTTGGATCGCACCATTAAgtatggtttt ... attgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtaatatttcccacacctagtatatgtctgttaatatgatgtgattgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCCTGAAGAGAAATATACGAATGCATTTCTTGGGTTTGGACCTGAGGACACC
                              tgttaat  putative branch site (score: 3)
                                ttaatatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggttttgtgctagaagtaatatttcccacacctagtatatgtctgttaatatgatgtgattgtggcagATGTTACACAGAATGCTTTGGAATGAAATTACTGAGGAAAAGAGATGTGCCTGAAGAGAAATATACGAATGCATTTCTTGGGTTTGGACCTGAGGACACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA