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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgatttatgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC

Basic information

species Oryza sativa
transcript LOC_Os01g17170.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G043109_T01 (Zea mays), 3'ss of exon 2
gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgatttatgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                                                                       | |      |   ||   | || ||  |   | | |||||     ||     |           || |||||| |||||   |     ||||||   ||||  ||||| ||||||||||| |||||||| ||||||||||| |||||||| |||||| | |||||||||||||||||||||||||||||||||||||||||||||
-------------------------------------------------------------------------------------catgcatgttttcctgattgtgttcaatttgaggctctagggtaatgatgagggcatgg-------agaaattcagctgaaagtttcatgtgatttgcactgtgtagGTTTTTGAACAAGGGTCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTCACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgatttatgct----gttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                                                                                             || ||  |    |||     ||  |||  |  || | | |  || |||||| |||||   |     ||||||   ||    ||| |||||||||||||||||||||||||| ||||||||||| |||||||| |||||| |||||||||||||||||||||||||||||||||||||||||||||||
------------------------------------------------------------------------------------------------------------gtacgcacctacctta-----tctcttttcatccattcggg-gagaaattcagctgaaagtttcatgtgatttgcactcactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 2
gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagc-ttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctg-catgattt--atgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                                                                                ||  ||||    ||  || || | ||||      ||| | |    |    | | |    |  |    || | ||  || | | ||||  || |||| |||||| |||||||||||  | ||||||||||| ||||| |||||| | || ||||||||||| ||||| || ||||| || |||||||| ||||| ||||||
-----------------------------------------------------------------------------------------------gtatggaaacgccttgtgcctttaatttttaattatccttctttgattttct-atttgatatcttgtttgtagtgcatgacctcattttgattctgtgcagGTTTTTGAACAAGGGTTTATCTGATTTCAATTTGGCTCTGGACTTGGGTTTCTTGACCAAAGCTAGAAAATACACATTTTTCAAGCCAAAGTTTATCTTC

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA19G30350.1 (Glycine max), 3'ss of exon 2
gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgattt--atgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                                                              || ||         || ||  |    ||  ||||   ||| | ||       | |||| |  ||  | |  | |    ||    || || | || ||| ||||  || |||| |||||| |||||||| ||  | |||||||| || ||||| |||||| | || ||||||||||| ||||| || ||||| || |||||||||||||| ||||||
----------------------------------------------------------------------------gtatggacacaccttgtgccttta----attcttaattctcattctttcatttcctatttgatatc--tcgtttgaatgtttgttgtgtatggcct-cattattttgattctgtgcagGTTTTTGAACAAAGGTTTATCTGATTTTAATTTGGCTCTGGACTTGGGTTTCTTGACCAAAGCTAGAAAATACACATTTTTCAAGCCCAAGTTTATCTTC

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgatttatgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                                                                                       || || |   ||| |   | ||| | ||  |||  | ||       ||||   ||||| |    ||     || |  | |  |   ||||||||||||||||||  ||||||||||||||||||| || ||  | || ||| |||| ||||| ||||| ||||| ||||||||||| || |||||||||
-----------------------------------------------------------------------------------------------------gtaagatct---cttaacactaaggacctctctttttaatc-------taagtgtttcaattttgatg-----ataaactttttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTTCCTGACAAAGGCAAGGAAATACACTTTCTTCAAGCCAAAATTCATCTTC

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0040g00390.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgatttatgctgtt-cagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                       |   | ||||     |  |   |  || |    |||||   | |  || | |||   | |  | || |  |||  | ||| | | | |      ||| |   |  || | | |  | |   |   |||   || ||||  || ||||||| ||| ||  ||||||| ||  | ||||||||||| |||||  ||||| | |||||| | || |||||||| ||||||||||| || ||||||||||||||||||
-------------------------------------gtatgcaaacaactctctgcccttctcccttcctcactcatggtcatatgcatcatagtttgc-agaacaagtaa--tacagctgttgag------ttttatagcttttaactgaaaagtctga---aataaacttcatg--ttctgctgttgcagATTTCTGAACAAAGGTTTATCTGATTTCAATTTGGCTTTGGACTTGGGGTTCCTCACAAAGGCTAGAAAGTACACCTTTTTTAAGCCCAAGTTCATCTTC

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ28505 (Selaginella moellendorffii), 3'ss of exon 2
gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgatttatgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC--------------------------------------------------------------
                                                                   ||   | | |   | | ||| |  |  |  |  ||  || |   |                                                                                                      || || |||||||| ||||| || || ||  ||||||| ||  ||||||||||||||||||||||  |||||||||||                                                              
------------------------------------------------------------------gttctcagtta--ctcagctggaaaaaaagcatcgatcatttcctatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncgactttaacttggctctggatcttggatttctgaccaaagCCCGGAAGTACACCTTCTTCAAGCCACAGTTCATCTTCTACGCGACGTATCTCTCGGAGAAGATCGGCTACTGGAGGTACATTACTATCTACAGGCACTT

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ30397 (Selaginella moellendorffii), 3'ss of exon 2
gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaat-tcaactgaattgtctgcatgatttatgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                                                                                                          || |   ||  ||||   ||| |||   ||  |   || |    |||  ||  ||| || ||       |||||| ||||||| ||  | || || || |||||||| ||||| || || ||  ||||||| ||  ||||||||||||||||||||||  |||||||||||
-------------------------------------------------------------------------------------------------------------------------gtaagttctcagtttc---tcagttggaaaaaaagcatcgatc--atttcctatatg-ttcat-------agGTTCCTGAACAAAGGATTATCCGACTTTAACTTGGCTCTGGATCTTGGATTTCTGACCAAAGCCCGGAAGTACACCTTCTTCAAGCCACAGTTCATCTTC

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|29662324|gb|CB658599.1|CB658599
EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
EST: gi|300216174|gb|HO087959.1|HO087959
EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
EST: gi|29672478|gb|CB668753.1|CB668753
EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
EST: gi|66912779|gb|CX099627.1|CX099627
EST:     GTGGCTGAGATCTTCTCGCTCATGTCCANGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
EST: gi|38474941|gb|CF959074.1|CF959074
EST:     GTGGCTGAGATCTACTCGCTCATGTCCANGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTAGATTTCAACTTGGCACTGGACCTCGGGT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCT-GATTTCAACTTGGCACTGGACCTCGGGT
EST: gi|29676338|gb|CB672613.1|CB672613
EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
EST: gi|38471854|gb|CF955985.1|CF955985
EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
EST: gi|33674878|gb|CF303117.1|CF303117
EST:     CGGCACGAGGG                         GTTCTTGAAC-AGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: CGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
EST: gi|38476267|gb|CF960400.1|CF960400
EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
EST: gi|38473793|gb|CF957925.1|CF957925
EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
EST: gi|29619025|gb|CB624037.1|CB624037
EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
EST: gi|38475252|gb|CF959385.1|CF959385
EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
EST: gi|29616676|gb|CB621688.1|CB621688
EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
EST: gi|38474054|gb|CF958186.1|CF958186
EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
EST: gi|29663604|gb|CB659879.1|CB659879
EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
EST: gi|2801122|gb|AA754416.1|AA754416
EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
EST: gi|29620880|gb|CB625891.1|CB625891
EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactcaattgagtaagcaattcaactgaattgtctgcatgatttatgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                     atgatttat  TA-rich tract