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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGGAAAGGAGACTTCGAGACACTAGAGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaattataatatacgcatttaacttcatagtataatagaaatatctttgggttgatgattgctcatttttaactttgctttcatgtgatttctcaatacag

Basic information

species Oryza sativa
transcript LOC_Os07g47290.3
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47290.3 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G544990_T01 (Zea mays), 5'ss of exon 14
GCTGGGAAAGGAGACTTCGAGACACTAGAGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaattataatatacgcatttaacttcatagtataatagaaatatct--ttgggttgatgattgctcatttttaactttgctttcatgtgatttctcaatacag
||| ||||||||||||| ||||| ||||| ||||||||||| ||||||||||| |||  |||| |||| ||||||||||||| || | | | | | || || |           ||    |     |  ||  || |||   | ||      |     |  | ||    ||    || |         
GCTAGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGTGAGCCCGCTGTTGCATCCGGCAAGCAGgtaaatgtattgacagtctaggcgtcctctccacctgtgcgctgatggttgctgattaggtatgtcatgat--gtgcaggaaatggcggagattctgttcca--------

upper sequence: LOC_Os07g47290.3 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G081682_T01 (Zea mays), 5'ss of exon 20
GCTGGGAAAGGAGACTTCGAGACACTAGAGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaattataatatacgcatttaacttcatagtataatagaaatatctttgggttgatgattgctcatttttaactttgctttcatgtgatttctcaatacag
||||||||||||||||| ||||| ||||| ||||||||||| ||||||||||| |||| |||| |||| ||||| ||||||| ||   | | | | || || |    || ||                 | ||| | ||||| ||||| |   |||  | ||   | ||||| ||||    | |||
GCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgttgacagtctaggcgtcct-ctccac----------------cattgcgctgatggttgctta---ttaggtatgtcatgatgtgctttcctg-tgcag

upper sequence: LOC_Os07g47290.3 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G313536_T01 (Zea mays), 5'ss of exon 14
------------------------------GCTGGGAAAGGAGACTTCGAGACACTAGAGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaattataatatacgcatttaacttcatagtataatagaaatatctttgggttgatgattgctcatttttaactttgctttcatgtgatttctcaatacag
                              ||| ||||||||||||| ||||| ||||| ||||||||||| ||||||||||| |||  |||| |||| |||||||||| || || | | | | | || || |    || ||                 || || | ||||| ||||| |   |||  | ||   | |||||              
GTTGTAACATTGCTCTATGGCTTCAATCAGGCTAGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGgtgagcccgctgttgcatccggcaagcaggcaaatgtattgacagtctaggcgtcct-ctccac----------------ctgtgcgctgatggttgctga---ttaggtatgtcatgatgtgcag-----------

upper sequence: LOC_Os07g47290.3 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G005493_T01 (Zea mays), 5'ss of exon 20
GCTGGGAAAGGAGACTTCGAGACACTAGAGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaattataatatacgcatttaacttcatagtataatag-aaatatctttgggttgatgattgctcatttttaactttgctttcatgtgatttctcaatacag
||||||||||||||||| ||| | |||||||||||||| || ||||||||||| |||| |||||| || ||||| |||||||||             |||| | || |   |    | ||||  ||||| |  ||   || |||| ||  || |  |    |||      ||| ||||   || |||
GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactc-----------cacgcgtatagcagta-gcaacaataacaaatacccgtg---tgctgatcgcatatatc-attcatgc-----ggtgctttcctgatgcag

upper sequence: LOC_Os07g47290.3 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G335948_T01 (Zea mays), 5'ss of exon 2
GCTGGGAAAGGAGACTTCGAGACACTAGAGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaattataatatacgcatttaacttcatagtataatagaaatatctttgggttgatgattgctcatttttaactttgctttcatgtgatttctcaatacag
||| ||||||||||||| ||||| ||||| ||||||||||| ||||||||||| |||  |||| |||| ||||||||||||| || | | | | | || |  |           ||    |     |    |||  | | |   |  | || |  |           |  |  | |  ||      
GCTAGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGTGAGCCCGCTGTTGCATCCGGCAAGCAGgtaaatgtattgacagtctaggtgtcctctccacctgtgcgctgatggt--tgttgattaggtatatcatgatgtgcaggaactggcggagattctgttcca------

upper sequence: LOC_Os07g47290.3 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G427620_T01 (Zea mays), 5'ss of exon 10
GCTGGGAAAGGAGACTTCGAGACACTAGAGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaattataatatacgcatttaacttcatagtataatagaaatatctttgggttgatgattgctcatttttaactttgctttcatgtgatttctcaatacag
||| ||||||||||||| ||||| ||||| ||||||||||| ||||||||||| |||  |||| ||||||||||||||| || || | | | | | || || |    || ||                 || || | ||||| ||||| |   |||  | ||   | |||||              
GCTAGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGgtgagcccgctgttgcatctggcaagcaggcaaatgtattgacagtctaggcgtcct-ctccac----------------ctgtgcgctgatggttgctga---ttaggtatgtcatgatgtgcag-----------

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|88518358|gb|CI446012.1|CI446012
EST:     AGAAGAANGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGGTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|15854754|gb|BI807566.1|BI807566
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCCTTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|88540647|gb|CI468708.1|CI468708
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|88974071|gb|CI002733.1|CI002733
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|89179716|gb|CI043995.1|CI043995
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|38476165|gb|CF960298.1|CF960298
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|88321906|gb|CI673054.1|CI673054
EST:     GGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: GGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|89194258|gb|CI116695.1|CI116695
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|88828748|gb|CI073618.1|CI073618
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|88514668|gb|CI442174.1|CI442174
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|29688817|gb|CB685092.1|CB685092
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|163927225|gb|EG710263.1|EG710263
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCT
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCT
EST: gi|88985909|gb|CI033238.1|CI033238
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|88506732|gb|CI434238.1|CI434238
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGGTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCNTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|12622806|gb|AU173019.1|AU173019
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|218483389|gb|FG947207.1|FG947207
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|88840977|gb|CI000939.1|CI000939
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|58031342|gb|CX728885.1|CX728885
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTTTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|88537783|gb|CI466758.1|CI466758
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|88475673|gb|CI412944.1|CI412944
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|66925796|gb|CX112644.1|CX112644
EST:     GGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: GGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|88995441|gb|CI022764.1|CI022764
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|88437040|gb|CI523990.1|CI523990
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|88535496|gb|CI464300.1|CI464300
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|313080767|gb|HO213564.1|HO213564
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC
EST: gi|88504210|gb|CI431716.1|CI431716
EST:     AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAG                         GAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCAGTGGTGC
genomic: AGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaa ... ctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGGAAAGGAGACTTCGAGACACTAGAGAAGAAGGTTCTGGAGTGGGGTGAACCCATTGTTCCATCTGGCAAGCAGgtaactggaattataatatacgcatttaacttcatagtataatagaaatatctttgggttgatgattgctcatttttaactttgctttcatgtgatttctcaatacag

- - - - - - - - - - - - - - - AAGAAG