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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgtacaatgcatttctgcgcaagtattcatgctcttttcagtcattcatattcattagattttgaaaagtactgatgtttctttgcttttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGTAGACTGTCTTCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCA

Basic information

species Oryza sativa
transcript LOC_Os03g17710.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17710.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G099317_T02 (Zea mays), 3'ss of exon 1
actgtacaatgcatttctgcgcaagtattcat-gctcttttcagtcattcatattcattagatt-ttga--aaagtactgatgtttctttgcttttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGTAGACTGTCTTCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCA
|||  || ||   | |    |||| |     | | |  |||| |||| |  |||||||||  || ||||  |||   |||||  |  ||| ||| ||       || |||||||||||||||||||  |||||| |||| |||||||||||||| ||| || |  | || ||||||||||||||  |||||||||| |||||  
actcaaccatat-tgttgatgcaatttggtgtagttgctttctgtcactt-tattcattaagttcttgatgaaacagctgatagtatttttcttgtggacagGAGATATGCCTCGCTATGATGATCGCTATGGAGGCACGCGCTTGTATGTTGGCAGATTGGCCCCCCGTACTCGTTCTCGTGATTTAGAATATCTCTTCGG--

upper sequence: LOC_Os03g17710.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G099317_T03 (Zea mays), 3'ss of exon 1
actgtacaat-gcatttctg-cgcaagtattcat-gctcttttcagtcattcatattcattagatt-ttga--aaagtactgatgtttctttgcttttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGTAGACTGTCTTCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCA-
      |||    |||  ||  |||| |     | | |  |||| |||| |  |||||||||  || ||||  |||   |||||  |  ||| ||| ||       || |||||||||||||||||||  |||||| |||| |||||||||||||| ||| || |  | || ||||||||||||||  |||||||||| ||||||| 
------caaccatattgttgatgcaatttggtgtagttgctttctgtcactt-tattcattaagttcttgatgaaacagctgatagtatttttcttgtggacaggagATATGCCTCGCTATGATGATCGCTATGGAGGCACGCGCTTGTATGTTGGCAGATTGGCCCCCCGTACTCGTTCTCGTGATTTAGAATATCTCTTCGGCAA
















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|33654664|gb|CF277278.1|CF277278
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|88422877|gb|CI615177.1|CI615177
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|58673537|gb|CK062223.1|CK062223
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|58653740|gb|CK042420.1|CK042420
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|88573286|gb|CI664857.1|CI664857
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|33654208|gb|CF276822.1|CF276822
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|88327495|gb|CI646681.1|CI646681
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|88729424|gb|CI752934.1|CI752934
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|66917360|gb|CX104208.1|CX104208
EST:     TCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|218497275|gb|FG960321.1|FG960321
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|88572064|gb|CI663635.1|CI663635
EST:     GCGGCGCCGGCGCCGGNGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|109974555|gb|DT806973.1|DT806973
EST:     GCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|88349704|gb|CI632839.1|CI632839
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|58674796|gb|CK063483.1|CK063483
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|88328329|gb|CI651340.1|CI651340
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|117220967|gb|CT861417.1|CT861417
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|88720424|gb|CI743723.1|CI743723
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|88761659|gb|CI771215.1|CI771215
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|88424660|gb|CI606459.1|CI606459
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
EST: gi|88342002|gb|CI644339.1|CI644339
EST:     GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTG                         GAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT
genomic: GCGGCGCCGGCGCCGGCGTACCGCTGCTTCCGCCGCATCCTCTATCTCTGgtgagcgtcc ... ttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcatattcattagattttgaaaagtactgatgtttctttgcttttgttttcagGAGATGCCTCGCTATGATGATCATTATGGAAGCACACGCTTGTATGTTGGTAGACTGTCTTCGCGCACTCGTTCTCGTGACCTAGAATATCTTTTCGGCA
                          tactgat  putative branch site (score: 2)
                                tgtttctttgcttttg  CT-rich tract
     tattcattagatttt  TA-rich tract