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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcaatgatggctgtgcacgtccaaagtttcagttttgtgcttacatatcaagatgttttgtctctttcgattgtcactgaattcttatatgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT

Basic information

species Oryza sativa
transcript LOC_Os01g44040.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g44040.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 14
tggcaatgatggctgtgcacgtccaaagtttcagttttgtgcttacatatcaagatgttttgtctctttc-gattgtcactgaa---ttcttatatgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT
     || | |      ||     |||| ||    |        ||   | ||     ||   |||  |  || |||   |||    ||| | | ||||||||||||||||||||| ||||| ||||| || |||||||| ||| | || ||||  || ||  |||||||||| |||||  | || || |||||  |  ||
----gatcaagaacaaacattggaaaagattataatggaacgaaactcgtaaacgaacttcaactcagtaagagtgtacttgataatttcctctttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT

upper sequence: LOC_Os01g44040.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 14
tggcaatgatggctgtgcacgtccaaagtttcagttttgtgcttacatatcaagatgttttgtctctttc-gattgtcactgaa---ttcttatatgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT
     || | |       |     |||| ||    |        || |   ||     || | ||   |  || |||   |||    ||| | | ||||||||||||||||||||| ||||| ||||| || |||||||| ||| | || ||||  || ||  |||||||||| |||||  | || || |||||  |  ||
----gatcaagaacaaagataggaaaagattataatgaaacgaaacgtgcgaacgaacttcgactaagtaagagtgtacttgataatttcctctttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT

upper sequence: LOC_Os01g44040.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA05G25780.2 (Glycine max), 3'ss of exon 14
tggcaatgatggctgtgcacgtccaaagtttcagttttgtgcttacatatcaagatgttttgtctctttc-gattgtcactgaa---ttcttatatgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT---
     || | |      ||     |||| ||    |        ||   | ||     ||   |||  |  || |||   |||    ||| | | ||||||||||||||||||||| ||||| ||||| || |||||||| ||| | || ||||  || ||  |||||||||| |||||  | || || |||||  |  ||   
----gatcaagaacaaacattggaaaagattataatggaacgaaactcgtaaacgaacttcaactcagtaagagtgtacttgataatttcctctttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTTGTA

upper sequence: LOC_Os01g44040.3 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 14
tggcaatgatggctgtgcacgtccaaagtttcagttttgtgcttacatatcaagatgttttgtctctttcgattgtcactgaattcttatatgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT
                                 ||||  |   |     | ||  | ||             |||| |    |     |      | ||| || ||||||||| ||||||| |||||||||||||||||| | |||||||| |||||  ||||||| || |||||  | || || |||||  | |||
---------------------------------gtttgttttctgtgacttaatcttttcctggaagcgtatttgttaaatcaaagacaccaattttcagATCAAACATGCCTGACGGGCAACCAAAATGGCTTCTCTCTATTATTCCGGGATACCCTATGCTCAATTTCATGCTGACAACTGCTATATACGTCCTT

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|86885457|gb|CI318608.1|CI318608
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCACCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88995453|gb|CI022776.1|CI022776
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88513138|gb|CI440644.1|CI440644
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88502372|gb|CI429878.1|CI429878
EST:     TACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: TACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88477010|gb|CI414281.1|CI414281
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGGCTTCTCTCTTTCATTCCGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAAT-GGCTTCTCTCTTTCATTCCGG
EST: gi|88560911|gb|CI491614.1|CI491614
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|29659100|gb|CB655375.1|CB655375
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88322184|gb|CI537767.1|CI537767
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88846659|gb|CI373427.1|CI373427
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88515591|gb|CI443245.1|CI443245
EST:     GGCAAGATTACTGTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|86498852|gb|CI141485.1|CI141485
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|89177189|gb|CI043692.1|CI043692
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88517436|gb|CI445090.1|CI445090
EST:     GGCAAGATTAGTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|86502826|gb|CI145459.1|CI145459
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88956170|gb|CI092458.1|CI092458
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88507120|gb|CI434626.1|CI434626
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatcaagatgttttgtctctttcgattgtcactgaattcttatatgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT
                                    aattcttatat  TA-rich tract