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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcaattcttagcgcataacatcttatcaacagaattacttggttatgtgtggtataattgaagatctcactctgtttatgccatgtgttgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCT

Basic information

species Oryza sativa
transcript LOC_Os08g09240.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g09240.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G134613_T01 (Zea mays), 3'ss of exon 1
tatcaattcttagcgcataacat-cttatcaacagaattacttggttatgtgtggtataattgaagatctcactctg--tttatgc-catgtgttgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCT
| |  ||  || |        || |  ||  ||| |  |||    |||| | | | || |  |||  ||||| | |   ||| | |  |||| || | |||||||||||||||| |||||||| ||||||||||||||||| || || || ||||| |||
tgtagatcttttggtttctttatacagatgtacata--tacccttttatct-tagaatgacagaat-tctcattatacatttgtacatatgttttatatcgcagAAAGGAGGCAAGCTGAGGCTAACCGCATCAGGGAGAAATACCCTGACAGAATCCCT

upper sequence: LOC_Os08g09240.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 2
--tatcaattc-ttagcgcataaca-tcttatcaacagaattacttggttatgtgtggtataattgaagatctcactctgtttatgccatgtgttgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCT
  | ||  |    ||  |||| |   | | ||    | |  |  ||  |   |  ||     ||| |  |  |   |||   | |    |   || | |  ||||||||||||| || || ||    |||||||||||||||||||| |||||||| || 
aatttctgtcagctattgcatgagggtttcatgggtaaatgtttttcttccagcatgt----atttagtaatttgttctaaatgtttttttccttatatgccagAAAGGAGGCAAGCAGAAGCTGCTCGCATCAGGGAGAAGTATCCTGATAGAATACCA
















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|55434634|gb|CV730441.1|CV730441
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|55436298|gb|CV731287.1|CV731287
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGATTCAGTCNGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|33659136|gb|CF281749.1|CF281749
EST:     TTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: TTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|58590250|gb|CF988558.1|CF988558
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|218487512|gb|FG953689.1|FG953689
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|25802781|gb|CA758742.1|CA758742
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|88721866|gb|CI743378.1|CI743378
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|88974162|gb|CI002783.1|CI002783
EST:     AGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: AGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|88428393|gb|CI564861.1|CI564861
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCATTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAAAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|58695129|gb|CK083816.1|CK083816
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|88963125|gb|CI026798.1|CI026798
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|33671347|gb|CF299586.1|CF299586
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCNATCAGGGAGAAGTATCCCGATAGA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGC-ATCAGGGAGAAGTATCCCGATAGA
EST: gi|58593892|gb|CF992200.1|CF992200
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCA-CCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|55431390|gb|CV728708.1|CV728708
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCATTTGCATCAGGGAGAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|218486561|gb|FG954049.1|FG954049
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|163926759|gb|EG715047.1|EG715047
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|33682438|gb|CF310677.1|CF310677
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|87012764|gb|CI295208.1|CI295208
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|58586677|gb|CF984985.1|CF984985
EST:     GGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAGGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: GGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|88424094|gb|CI689796.1|CI689796
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
EST: gi|58599898|gb|CK010426.1|CK010426
EST:     CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCG                         AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA
genomic: CAGGGCGCGCGTGATGGCGAGGAGCTCGTTCAAGCTGGAGCACCCACTCGgttcgtctca ... tgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtgtggtataattgaagatctcactctgtttatgccatgtgttgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCT
                    atctcac  putative branch site (score: 3)
         tataattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcaattcttagcgcataacatcttatcaacagaattacttggttatgtgtggtataattgaagatctcactctgtttatgccatgtgttgtgtcgcagAAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT