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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaataaaccttgattgttctctgttatctccagtttttgtttttaactgaaacaagtagcatctacaagatggccacatatatacttcacaact...

Basic information

species Oryza sativa
transcript LOC_Os02g56850.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56850.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM5G806449_T03 (Zea mays), 5'ss of exon 13
AAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaataaaccttgattgttctctgttatctccagtt-tttgtttttaactgaaacaagtagcatctacaagatggccacatatatacttcacaact----
|||||||||||||||||||||| |  ||| |||||| |||||||||| ||||||||||||||||||| || ||   || |||  |   | || |||   |   ||| ||||  | |  || |  ||   |  |  | ||   |||   || |||| ||| |||  |    
AAAACTGTGTTTGGTGGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcacacaatcttattcactttcagttgaatggtgttgtttgcatctttctaatccagcca--agttgca---tggttgcacatatgctttacagtttgca
















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

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTCgtaagccaataaaccttgattgttctctgttatctccagtttttgtttttaactgaaacaagtagcatctacaagatggccacatatatacttcacaact

- - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT