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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctcactattttttagataatggatagaaatccgatctctatatccacatgtaatatacccagctttcctcgctaatgcatattccgtccatgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCCAAGTACCTTCGTGGCTACTCCTTTCCGTTGTAATCCCAGGTCTTGTGAG

Basic information

species Oryza sativa
transcript LOC_Os02g39570.6
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G407044_T03 (Zea mays), 3'ss of exon 1
cctcactattttttagataatggatagaaatccgatctctatatccacatgtaatatacccagctt--tcctcgctaatgcatattccgtccatgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCCAAGTACCTTCGTGGCTACTCCTTTCCGTTGTAATCCCAGGTCTTGTGAG-
             |||||   |     | |||  |  |   ||   |  ||| | |   |    |   ||||| | | ||  | || ||  ||||   ||||||||||||||| || ||||| || ||||||||||||||    || || ||||||||||| || ||||||||  ||||  ||||  ||  |   | ||||  
------------gtagattgggtcctcacatc-aacttaactacttaagtgtgaaaaggcagattgggtcctcaccattg--tgttgcgcacatg---acagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCCAAGTACCTCCGCGGCTACTCTCTTCCACTGTAG-CCTTGCAGTCGTGATG

upper sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 11
-------------------------------------------------cctcactattttttagat-aatggatagaaa-tccgatctctatatccacatgtaatatacccagctttcctcgc-------taatgcatattccgtccatgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCCAAGTACCTTCGTGGCTACTCCTTTCCGTTGTAATCCCAGGTCTTGTGAG-
                                                   |       |||  ||| |||| | ||  | |||  | | | |  ||  | ||  | |     |  |||    |       | |    | ||  |  ||  |  ||||||||||||||| || |||||||| |||||||| |||||    ||||| ||||||||||| || || |||||  |||| |||||  ||  |   ||||||  
gtatgtttcttatcactccacatgaacttaactaaagtgtgaaaatgcagtttgggtcctttgggatgaatgaacagtcactcctttttatctgaccctaggtgttgttttgtgtgttctgtacacggtcctcaccattgttttgcacac-atgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCCAAGTACCTCCGCGGTTACTCTCTTCCATTGTAG-CCTGGCATTTGTGATT

upper sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT2G31810.3 (Arabidopsis thaliana), 3'ss of exon 10
--cctcactattttttagataatggatagaaatccgatct-ctatatccacatgtaatatacccagctttcctcgctaatgcatattccgtcca--tgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCCAAGTACCTTCGTGGCTACTCCTTTCCGTTGTAATCCCAGGTCTTGTGAG
   ||     || | |  | ||     | ||    ||    | ||  | || |  |   ||  ||      |  | | | || ||||  |  ||    | ||||||| || ||||| || || |||||  |||  || ||||| || || || ||||||||||||||||| ||||||||||| ||   |  | |   | |   ||
cttcttctggttgtgtgtagaacaagaataagcttgacaagccatgactactttcagattatgca-----tcgtgttgacgcttattatgaacaatcaatcacagGTTGCAAGAACCGGTCGTGTGGCATTGGCTCGTGAATCGGGAGTGGACTCCAAGTACCTTCGTGGATACTCCTTTCCTTTAACAGGCTAAACCGTTGCAG

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|88488548|gb|CI425819.1|CI425819
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88539198|gb|CI468290.1|CI468290
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTTGTCCGCGAATCCGGTNTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|29676546|gb|CB672821.1|CB672821
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88538414|gb|CI467440.1|CI467440
EST:     ACAAGATGNTTGCATTACAAAGGCTNTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88477271|gb|CI414542.1|CI414542
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTNTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88512954|gb|CI440460.1|CI440460
EST:     CAANATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: CAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTAT-GGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88543743|gb|CI473778.1|CI473778
EST:     ACAAGATGGTTGCATTACAAAGGCTNTTGGACCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88284518|gb|CI405964.1|CI405964
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGGACAGGGCGAGTGGCGCTGGTCCNCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88832223|gb|CI017457.1|CI017457
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|15853702|gb|BI806498.1|BI806498
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88478672|gb|CI415943.1|CI415943
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88906495|gb|CI375567.1|CI375567
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGGGGTCGATTC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCC-GGTGTCGATTC
EST: gi|32948291|gb|BP184863.1|BP184863
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88508589|gb|CI436095.1|CI436095
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCNCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|86506103|gb|CI148736.1|CI148736
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88475065|gb|CI412336.1|CI412336
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         TTCGCCAGAACAGGGCGANTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|86522997|gb|CI163203.1|CI163203
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88481174|gb|CI418445.1|CI418445
EST:     ACAAGATGGTTGCATTACAAAGGGTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGTTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|33682201|gb|CF310440.1|CF310440
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88502715|gb|CI430221.1|CI430221
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         TTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88552259|gb|CI480930.1|CI480930
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88527127|gb|CI455250.1|CI455250
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         TTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTTTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|87021293|gb|CI295352.1|CI295352
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88273463|gb|CI393869.1|CI393869
EST:     ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
EST: gi|88513717|gb|CI441223.1|CI441223
EST:     ACAAGATGGTTNCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG                         GTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC
genomic: ACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaa ... atgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatgtaatatacccagctttcctcgctaatgcatattccgtccatgaccacagGTCGCCAGAACAGGGCGAGTGGCGCTGGTCCGCGAATCCGGTGTCGATTCCAAGTACCTTCGTGGCTACTCCTTTCCGTTGTAATCCCAGGTCTTGTGAG
                         cgctaat  putative branch site (score: 3)
      taatata  TA-rich tract