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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatttttacttagcctttttattttttattcatcatcagtgttgtgtggtgttcaaatgcatattctacacaaatcaggatcctttcaaagaga...

Basic information

species Oryza sativa
transcript LOC_Os05g22970.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g22970.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G125310_T01 (Zea mays), 5'ss of exon 7
GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatttttacttagcctttttattttttattcatcatcagtgttgtgtggtgttcaaatgcatattctacacaaatcaggatcctttcaaagaga---------
|||||||||||||||||||  | |||||| | ||||| ||||| || || |||||||||||||| |||||||| || || || ||||||||||  | |||||        |||| || | ||  |  | ||| |   ||   | ||  | ||||     ||||  |  | |             |  | |         
GTCATATAGGAGTAACTGTGGATGATGTCCACAAGGCATGTGAACGCTTTGAACGTCTTGGGGTTGAGTTTGTGAAGAAACCTGATGATGgtaggtgattttg-------ctttgtagtgttactcaaacatgaaaattaaatagt--taaaatcttctttctgtaagatttgcagggtaactgagcatattacgactg

upper sequence: LOC_Os05g22970.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA12G08470.1 (Glycine max), 5'ss of exon 7
GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatttttacttagcctttttattttttattcatcatcagtgttgtgtggtgttcaaatgcatattctacacaaatca--ggatcctttcaaagaga---------
| || || ||  |||||||| | ||    || ||||| |||||  | ||  |   ||| || || ||||||||||| |||||||||||||||||   ||||||  ||||        ||||  ||||||    |||| ||     ||  || || |   || |  | | ||||  | ||  ||| | ||  |         
GACACATTGGTATAACTGTTGATGACACATACAAGGCATGTGAAAGATTTCAGAATCTGGGAGTTGAGTTTGTTAAGAAGCCAGATGATGgtaa-caatttttctttag--------ttttcaattcatt-ctagtggtgcccactgcccatatacg-gttgtgaatatatcattgtatttttttacagctatgaattgtt
















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|88981533|gb|CI027151.1|CI027151
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|33818513|gb|CF335087.1|CF335087
EST:     TGAGCGGTTCGAACGTCTTGNGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|88969340|gb|CI382888.1|CI382888
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTCCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|33819107|gb|CF335378.1|CF335378
EST:     GAGCGGTTCGAACGTCTTGGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: GAGCGGTTCGAACGTCTTGGGG-TAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|89192212|gb|CI393569.1|CI393569
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|87026661|gb|CI254767.1|CI254767
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|86484436|gb|CI127069.1|CI127069
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGGTGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|88489735|gb|CI427007.1|CI427007
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|88282810|gb|CI402010.1|CI402010
EST:     GGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: GGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|87034760|gb|CI189384.1|CI189384
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|86846361|gb|CI280742.1|CI280742
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|88201878|gb|CI202233.1|CI202233
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|25800681|gb|CA756642.1|CA756642
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCANAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|33819105|gb|CF335377.1|CF335377
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|88473597|gb|CI410868.1|CI410868
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|86599770|gb|CI255932.1|CI255932
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|88202210|gb|CI202565.1|CI202565
EST:     TGATCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|88506478|gb|CI433984.1|CI433984
EST:     TGAGCGGTTCGAACTTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|33813839|gb|CF332805.1|CF332805
EST:     GAGCGGTTCGAACGTCTTGGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: GAGCGGTTCGAACGTCTTGGGG-TAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|58687672|gb|CK076359.1|CK076359
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|88264338|gb|CI368112.1|CI368112
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGATTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|33815680|gb|CF333691.1|CF333691
EST:     GAGCGGTTCGAACGTCTTGGGGTANAAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: GAGCGGTTCGAACGTCTTGGGGTAGA-GTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|86536276|gb|CI176482.1|CI176482
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|33813841|gb|CF332806.1|CF332806
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|88849383|gb|CI089291.1|CI089291
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|86496472|gb|CI139105.1|CI139105
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|86593628|gb|CI264507.1|CI264507
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|88257463|gb|CI359851.1|CI359851
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|88447060|gb|CI531303.1|CI531303
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTT-AAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGGTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|58692806|gb|CK081493.1|CK081493
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|86511468|gb|CI154101.1|CI154101
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|15846828|gb|BI795104.1|BI795104
EST:     TGA-CGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAA-GGCATTGCATTTATC-AAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
EST: gi|33815682|gb|CF333692.1|CF333692
EST:     TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATG                         GTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG
genomic: TGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatt ... ttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATATAGGAGTAACTGTTCACGATGTCTATAAGGCGTGTGAGCGGTTCGAACGTCTTGGGGTAGAGTTTGTTAAAAAGCCAGATGATGgtaaattatttttacttagcctttttattttttattcatcatcagtgttgtgtggtgttcaaatgcatattctacacaaatcaggatcctttcaaagaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG