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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaatactccctatgcgtgttccaaactagtatattgcaaccagttacggcccgattgcgcaatagacctaactctttttcttgctctgttctgcag

Basic information

species Oryza sativa
transcript LOC_Os06g35030.3
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g35030.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G814159_T01 (Zea mays), 5'ss of exon 9
GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaatactccctatgcgtgttccaaactagtatattgcaaccagt-tacggcccgattgcgcaatagacctaactctttttcttgctctgtt-----ctgcag
|||||   ||||||||| |||||||  ||||||||||| || |||||| ||||||| || ||||||| | ||| |  ||    ||| ||  || |  |  ||       ||  | |    |      |   |    || ||||| |    ||  |||||      |||||
GCAGATAGTGCTATTCTCGCTCTGAACTGCAGTGGCATTGTTCTTGGAACGCTTCCTGTTAGgcaagaacatattttctgcatgtgctcggaagttctg-atcatggtaagggtgcctgtctcccatgtttttttgcttactctctgctctgtactgttggtttttgcag
















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|58610994|gb|CK038706.1|CK038706
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTGCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|86498038|gb|CI140671.1|CI140671
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|88199202|gb|CI199052.1|CI199052
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCTAAAGACACCGGTCCGGCCCCGTCCGCCCCGTGTGACGT
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTC-AAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGT
EST: gi|87007992|gb|CI296970.1|CI296970
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|88247552|gb|CI247401.1|CI247401
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|87025635|gb|CI250129.1|CI250129
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|88217232|gb|CI217081.1|CI217081
EST:     GTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: GTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|29664696|gb|CB660971.1|CB660971
EST:     ATTCTTGCTATGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|88246608|gb|CI246457.1|CI246457
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|88249302|gb|CI249151.1|CI249151
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|218500791|gb|FG960831.1|FG960831
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCG
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCG
EST: gi|29664748|gb|CB661023.1|CB661023
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|86593985|gb|CI260214.1|CI260214
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|87035568|gb|CI190190.1|CI190190
EST:     GCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: GCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|88247664|gb|CI247513.1|CI247513
EST:     CATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: CATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|86495703|gb|CI138336.1|CI138336
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|88243612|gb|CI244009.1|CI244009
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|29673490|gb|CB669765.1|CB669765
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|88249620|gb|CI249469.1|CI249469
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|29637104|gb|CB642113.1|CB642113
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|396941304|gb|HO188513.1|HO188513
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|29664747|gb|CB661022.1|CB661022
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|88236140|gb|CI235342.1|CI235342
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|38476666|gb|CF960799.1|CF960799
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|88250150|gb|CI249999.1|CI249999
EST:     TTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: TTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|87022101|gb|CI259173.1|CI259173
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|86539456|gb|CI179662.1|CI179662
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCTTCAG                         GTTGAGCCCGTCAAAGACGCCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|86535072|gb|CI175278.1|CI175278
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|88250034|gb|CI249883.1|CI249883
EST:     TGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: TGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|86417377|gb|CI031586.1|CI031586
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|29685221|gb|CB681496.1|CB681496
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|88238786|gb|CI238635.1|CI238635
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
EST: gi|5003290|gb|AU068439.1|AU068439
EST:     ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG                         GGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC
genomic: ATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 72 (upstream exon), 65 (downstream exon)
Score: 18

GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaat ... tgttctgcagGGTGAGCCCGTCAAAGACACCGGTCCGGCCCCGTTCGCCCCGTGTGACGTCGCACTGAAACCCGGCTCTCTCATCTGAAGCCATCGTCCAGGGCAGCAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAGgcaagcaaatactccctatgcgtgttccaaactagtatattgcaaccagttacggcccgattgcgcaatagacctaactctttttcttgctctgttctgcag

- - - - - - - - - - - - - - - - - - - - -  TTGGAG