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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactgaatgatctagtgtttcatgtttaagaatttccttttgaattgagatggccttgtgcctttgtttcattatatagagaaaaaatgtatatct...

Basic information

species Oryza sativa
transcript LOC_Os12g04990.3
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 9
TAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaac--tgaatgatctagtgtttcatgt-ttaagaatttccttttgaattgaga---tggccttg----tgcctttgtttcattatatagagaaaaaatgtat-atct----------------------------------------------------
 | ||| |   |||| || ||||||||||| |||||||||||||||||| ||||| | |||||||| ||| |||| || || |||||||||||   || |   | |  | ||| ||   || |||| ||   ||      ||     |  |||||    |    ||| || |   | |    |     ||| | ||||                                                    
AAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAGgtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacacttttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaatttctcctggattttag

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 17
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 5'ss of exon 18
TAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactgaatgatctagtgtttcatgtttaagaatttccttttgaattgagatggccttgtgcct------ttgtttcattatatagagaaaaaatgtatatct
 | |||||   |||| || ||||| ||| | ||||||||||| |||||| ||||| |||| ||||| |||||||||||||| || ||||    |  ||  |||   || ||  | |       ||      | || | | ||  | | |  |        |      | |   ||  ||  | |   |     
GAAAGAGGTGATTGATGAAGATGGATGGCTTCACACTGGAGATATAGGTCTGTGGCTGCCGGGAGGACGTCTAAAAATTATTGACAGgtttt-ccaaaaaatcacttgattgttatcagctgtttcttcactaaaatcaaatctcttggctcacaaagaataagcctacttcttactgatgatacaaa-----
















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|29630787|gb|CB635796.1|CB635796
EST:     GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactga ... tggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
EST: gi|29625658|gb|CB630669.1|CB630669
EST:     GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactga ... tggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
EST: gi|58659745|gb|CK048425.1|CK048425
EST:     GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACAT
genomic: GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactga ... tggtctcaagGAAAAAGAACAT
EST: gi|29622085|gb|CB627096.1|CB627096
EST:     GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactga ... tggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
EST: gi|29626658|gb|CB631669.1|CB631669
EST:     AGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: AGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactga ... tggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
EST: gi|313081138|gb|HO213724.1|HO213724
EST:     GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactga ... tggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
EST: gi|29674288|gb|CB670563.1|CB670563
EST:     GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactga ... tggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactgaatgatctagtgtttcatgtttaagaatttccttttgaattgagatggccttgtgcctttgtttcattatatagagaaaaaatgtatatct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG