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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTTGATCATGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactcatcacataatgatcatctatctccttttcatttatctagcaacaagttttatgtattgtttatacag

Basic information

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

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04990.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA20G28200.1 (Glycine max), 5'ss of exon 6
CGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTTGATCATGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactcatcacataatgatcatctatctccttttcatttatctagcaacaagttttatgtattgtttatacag----------------------
 | ||||| ||||||||||| |||||||||||||||  ||| ||||||||||| ||  | ||||| |||| |||||| ||||| || ||||||||||| ||||||   ||  ||  | ||    |  | |||  || | |  |||||| |     |  |||  |   | ||  ||||                      
AGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTGCATACTCATTTGTATCAGTGCCTCTGTATGATACTCTTGgtatgttgtctacaatttatctggaaatttctt-ttcttacatatctacc--ttggccttaccttcagatttaacagcaagaaactgcttgttctgtag

upper sequence: LOC_Os12g04990.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA15G34650.1 (Glycine max), 5'ss of exon 2
----------------------CGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTTGATCATGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactcatcacataatgatcatctatctccttttcatttat-ctagcaacaagttttatgtattgtttatacag
                       | ||||| ||||||||||| |||||||||||||||  ||| ||||||||||| ||  | ||||| |||| |||    ||   | ||| || |||   |   ||           | ||| ||     | || ||| |||  ||| | | |   |  | | ||  || ||        
TTATGGAATCCAAAAGGGCTCTAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTGCATACTCATTTGTGCAAgttatattttgtg-tacctcaaacat----------taaaattattgctgagctacttgtcagatattccaactgtacatctaat-catggtag------

upper sequence: LOC_Os12g04990.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 6
CGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTTGATCATGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactcatcacataatgatcatctatctccttttcatttatctagcaacaagttttatgtattgtttatacag----------------------
 | ||||| ||||||||||| |||||||||||||||  ||| ||||||||||| ||  |  |||| |||| |||||| ||||| || ||||||||||| |||| ||  ||   |  | || |  |  | |||  || | |  | |||| |     |  |||  |  || ||  ||||                      
AGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTTCATACTCATTTGTATCAGTGCCTCTGTATGATACTCTTGgtacgctgtctataatttatcaggaaatttctt-ttcttacatgtctacc--ttggccttaccttctgatttaacagcaagaaattgcttgttctgtag

upper sequence: LOC_Os12g04990.4 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 6
CGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTTGATCATGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactca-tcacataatgatcatctatctccttttcatttatctagc---aacaagttttatgtattgtttatacag-------------------------------
 |  ||||  | |||||||| |||||||||||||||  ||| ||||||||||||||  | |||| |||||||||||| || ||  | ||||| ||||| |||  | | |   | |    || |   | ||||    |||    || || |    ||| | |  ||   ||    || |                                  
TGTGTTGGCCTATATTTTATCAACAGACCTGAGTGGCTCATTGTTGATCATGCCTGCTCTGCATTTTCATATGTATCAGTTCCTTTATATGACACTCTTGgttcgtaattggttattgtataaaactttatcggacttttgcctagcttggccaaaccactgctacaaatctactaaagcttaacaaagccttgataattgttgctctgcag

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|33675569|gb|CF303808.1|CF303808
EST:     TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAG                         GTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT
genomic: TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactc ... gtttatacagGTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT
EST: gi|58689916|gb|CK078603.1|CK078603
EST:     TGCCTGTGCGGCATA-TCATATGTATCCGTGCCACTTTATGATACTCTAG                         GTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT
genomic: TGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATACTCTAGgtatgcactc ... gtttatacagGTCCAGATGCAGTTCAGTTCATTGTTAACCATGCGACAGTACAAGCTATTT