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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattcagtgcatttatggctgctgctgctttctttagattatctgcttttccacaatcatcgtgtcactcataacatggtttctttttttgttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGAAGCCAAGAGCGATGTTCTTGTTTACACTTCCAGCTTCAACCCAATGAAG

Basic information

species Oryza sativa
transcript LOC_Os02g56850.4
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56850.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM5G806449_T03 (Zea mays), 3'ss of exon 13
tattcagtgcatttatggctgctgctgctttctttagattatctgcttt--tccacaatcatcgtgtcactc----ataacatggtttctttttttgttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGAAGCCAAGAGCGATGTTCTTGTTTACACTTCCAGCTTCAACCCAATGAAG
        |||  |||       | || | | || ||| ||| ||||||  |||  ||||||||  |||  |    ||||| |||||   | || | || ||| ||||| ||||||||||| ||||||||| | || ||| | ||||| ||||||||||| ||  | ||| ||||||||| ||  ||    |||||||||||||||
----tgacgcaaatattcagagaggtgttcttttaagaatatatgctttcctccttaatcatcg-atcatcctgtaataacttggttctctgttattttcaat-agCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGAAGCTAATGGTGATATTCTTGTTTTCATCTCATCATTCAACCCAATGAAG
















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|58692171|gb|CK080858.1|CK080858
EST:     GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTC                         CATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
genomic: GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
EST: gi|218503186|gb|FG945930.1|FG945930
EST:     GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTC                         CATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
genomic: GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
EST: gi|9886227|gb|AU102120.1|AU102120
EST:     GCCAGCCAACTAAACCTGATTACCAGAGATGTACCTTGTGCTGTTTTCTC                         CATCCCACCACTATCCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGG
genomic: GCCAGCCAACTAAACCTGATTA-CAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTAT-CAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGG
EST: gi|88217368|gb|CI217217.1|CI217217
EST:     AGATGTACCTTGTGCTGTTTTCTC                         CATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
genomic: AGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
EST: gi|27578226|gb|CB000921.1|CB000921
EST:     GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTC                         CATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
genomic: GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
EST: gi|29675049|gb|CB671324.1|CB671324
EST:     GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTC                         CATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
genomic: GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
EST: gi|87015137|gb|CI273535.1|CI273535
EST:     GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTC                         CATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
genomic: GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
EST: gi|86594898|gb|CI258152.1|CI258152
EST:     GGCCAGCCAACTAAACCTGATTACAGAGATGTATCTTGTGCTGTTTTCTC                         CATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
genomic: GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
EST: gi|33675534|gb|CF303773.1|CF303773
EST:     GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTC                         CATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
genomic: GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
EST: gi|58686026|gb|CK074713.1|CK074713
EST:     ACAGAGATGTACCTTGTGCTGTTTTCTC                         CATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
genomic: ACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
EST: gi|29625188|gb|CB630199.1|CB630199
EST:     GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTC                         CATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
genomic: GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
EST: gi|4714976|gb|AU056093.1|AU056093
EST:     GGCCAGCCAACTAAACCNGATTACAGANATGTACCTTGTGCTGTTT-CNC                         CATCCCACCACTATCAGTAGTGGGCTTGAGTGA
genomic: GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGA
EST: gi|86594937|gb|CI258191.1|CI258191
EST:     GGCCAGCCAACTAAACCTGATTACAGAGATGTATCTTGTGCTGTTTTCTC                         CATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
genomic: GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
EST: gi|87014199|gb|CI273389.1|CI273389
EST:     GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTC                         CATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
genomic: GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
EST: gi|396941644|gb|HO188301.1|HO188301
EST:     GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTC                         CATCCCACCACTATCAGTAGTGGGGCTTGAGTGAACAGCAGGCTTTGGAGG
genomic: GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGT-GGGCTTGAGTGAACAGCAGGCTTTGGAGG
EST: gi|88845181|gb|CI084106.1|CI084106
EST:     TGTGCTGTTTTCTC                         CATCCCACCACTATCAGTAGTGGGCTTGAGTGAACACCAGGCTTTGGAGGA
genomic: TGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
EST: gi|218481326|gb|FG969724.1|FG969724
EST:     GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTC                         CATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
genomic: GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
EST: gi|86430740|gb|CI083163.1|CI083163
EST:     GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTC                         CATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA
genomic: GGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaat ... gttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttccacaatcatcgtgtcactcataacatggtttctttttttgttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGAAGCCAAGAGCGATGTTCTTGTTTACACTTCCAGCTTCAACCCAATGAAG
                       tcataac  putative branch site (score: 2)
                                  tttctttttttgtt  putative PPT
                                      tttttttgttgaatta  TA-rich tract