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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttatttaatcctagtgttcttttcttacagactgtctatggaccttaattagttctgaaagatttgcgtaagtttttctatcattcagGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAAGGCACCTCATCTTTCTTCAACCATCCCTCCAAGCCTTCCTTGGAAATCT

Basic information

species Oryza sativa
transcript LOC_Os03g48300.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 12
---gtaatttatttaatcctagtgttcttttcttacagactgtcta---tggaccttaattagttctgaaagatttgcgtaagtttttctatcattca-gGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAAGGCACCTCATCTTTCTTCAACCATCCCTCCAAGCCTTCCTTGGAAATCT
    || ||| |  ||   |  | || | | || | | |   | ||   ||  ||| || |  || ||   |        |  || |  |   | | | |||||||||| ||| |||| ||  |  | || ||||| ||  |||||||||| |||||||||||||||||| | || || ||||   | || ||||||   
actatattttctgcaaatattttattttatactaataaatactatacgttgttcctcaactttttgtgctggtgaaaatcacattctgttgctactgaagGTATTATGATGATTCTGCCTGTGTTCTGCGGAAGATGTTGTTAGATGCAAAAGCACCTCATCTTTCTTCAGCAATTCCGCCAACTTTACCATGGAAAGTA

upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 11
-------------------------------------------------------------------gtaatt-tatttaatcctagtgttcttttcttacagactgtctatggaccttaattagttctgaaagatttgcgtaagtttt--tctatcattc----agGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAAGGCACCTCATCTTTCTTCAACCATCCCTCCAAGCCTTCCTTGGAAATCT
                                                                    |  || ||| ||    | |      ||  ||||| ||| | | || |   || |   |   |  | |||| | | | || |  | |   | |     ||||||||||| |||||||| ||  |  | |||||||| ||  |||||||||| |||||||||||||||||| | || || ||||   | || ||||||   
gtaatattttgtgatttattgttttggcactgttatatggttcaaaatgcatcaatagttattcactctgcttgtatctataattggaaaagcttatttaca-actctttttgcataata-tctttatggtgaaattttcatcatttctcgtttgctacttctgaagGTATTATGATGATGCTGCCTGTGTGCTGCGAAAGATGTTCTTAGATGCAAAAGCACCTCATCTTTCTTCAGCAATTCCACCAACTTTACCATGGAAAGTA

upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 9
---gtaatttatttaatcctagtgttcttttcttacaga--ctgtctatggaccttaa----ttagttctga-aagatttgcgtaagtttttctatcattcagGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAAGGCACCTCATCTTTCTTCAACCATCCCTCCAAGCCTTCCTTGGAAATCT
    || ||| |  ||   |  | || | | || | | |  || |  || |  |  ||    || || |||   | | |  | |   | | |   | ||  ||||||||||| ||| |||| ||  |  | || ||||| ||  |||||||||| |||||||||||||||||| | || || ||||   | |||||||||   
actatattttctgcaaatattttcttttatactaataaatactatacattgttcccaacatttttgtgctggtgaaaatcacat---tctgttgctaatgaagGTATTATGATGATTCTGCCTGTGTTCTGCGGAAGATGTTGTTAGATGCAAAAGCACCTCATCTTTCTTCAGCAATTCCGCCAACTTTACCTTGGAAAGTA

upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 12
---gtaatttatttaatcctagtgttcttttcttacagactg----tctatggaccttaattagttctgaaagatttgcgtaagtttttctatcattcagGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAAGGCACCTCATCTTTCTTCAACCATCCCTCCAAGCCTTCCTTGGAAATCT
     |   | | | ||| |  | | |  || |   |  ||     | |||  |  |  | |  |  | | | || |    |  | | | | ||  | |||||||| ||||||||||| ||  |  |||| || || ||| | ||||||||||| ||||||||||||||||| || ||||| |  || || ||||||   
gataaacactgtgtcatcgtcatatccacttttggaactctcagtttgtattcatttggagttttaatcagaaatgtcaccagatctctttctctgtaagGTATTACGACGATGCTGCTTGTGTGCTACGGAAAATGTTTTTGGATGCAAAGGCTCCTCATCTTTCTTCAACAATTCCTCCCATTCTGCCATGGAAAATC

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|29674285|gb|CB670560.1|CB670560
EST:     TCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA                         GTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAA
genomic: TCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaatttatt ... tatcattcagGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctatggaccttaattagttctgaaagatttgcgtaagtttttctatcattcagGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAAGGCACCTCATCTTTCTTCAACCATCCCTCCAAGCCTTCCTTGGAAATCT
         ccttaat  putative branch site (score: 4)
                                       tttttctatcattc  putative PPT
           ttaattagtt  TA-rich tract