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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgttaatacaagttggaggagatttctacaccaggtactaattctctatctcaatgacttttgcag

Basic information

species Oryza sativa
transcript LOC_Os12g04990.1
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04990.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 13
CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgttaata-caagt-tggaggagatttctacacc-aggtactaattctctatctcaatgacttttgcag--------------------------
|||||||||||||||||||| |||||||||   ||||| ||||| || |||||| | || |||||||||||||||||||| ||||||||||||||   | |  | | | | ||||| ||||  |  |  |  | || | |  ||||      | ||||||||                           
CTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTCACAGTGGACAATGGTCTCCTCACCCCAACATTCAAGgtaggccccccactggcgactctagaggaaatttacaagctgaaatgctgagtggctatg-----gccttttgcaccccctcccttctcaatacttgtgcag

upper sequence: LOC_Os12g04990.1 (Oryza sativa), 5'ss of exon 22
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 22
CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgttaat-acaagttggaggagattt--ctacaccaggtac----------taattctctatctcaatgacttttgcag-----------
 | |||||||||||||||||||||||||| ||  | ||   |||||| || ||  | || |||| ||| || || ||||| ||||||| | |      | | | || |  ||| | ||    | | | |||  ||           |      ||   || |  ||| |               
TTGAGAGGTTTTGAATTTGCCAAAGCTGTGACTTTGGTGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAGgcaagtgttcaatttaaaaatctgagaaaataaaaccagagcagacacaataaaatggcaggctcttactgcattatcttctttcatgttcttccag
















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|29630787|gb|CB635796.1|CB635796
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88512322|gb|CI439828.1|CI439828
EST:     CACATTAGAAAATGGTCCCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAGGAAATCGCAGATATG
genomic: CACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|86534809|gb|CI175015.1|CI175015
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|3767955|gb|AU031982.1|AU031982
EST:     TTGCTGANCCTTTCACATTANAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|29625658|gb|CB630669.1|CB630669
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|89185151|gb|CI050885.1|CI050885
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88487313|gb|CI424584.1|CI424584
EST:     TTGCTGGACCTTTCACATTAGGAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|29622085|gb|CB627096.1|CB627096
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|29626658|gb|CB631669.1|CB631669
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|86862496|gb|CI345563.1|CI345563
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|313081138|gb|HO213724.1|HO213724
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|25806439|gb|CA762400.1|CA762400
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88475891|gb|CI413162.1|CI413162
EST:     CCTTTCACATTAGGAAATGGTCCCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAGGGAAATCGCAGATAT
genomic: CCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAA-AGAAATCGCAGATAT
EST: gi|86870514|gb|CI320610.1|CI320610
EST:     TTGCTGAACCTTTCACATTAGAAAAT-GTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88273599|gb|CI394005.1|CI394005
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88509891|gb|CI437397.1|CI437397
EST:     TTGCTGAACCTTTCACATTAGGAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGGTAAGGCATACTTTGCAAAAGGAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|89184059|gb|CI046624.1|CI046624
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|86851406|gb|CI314004.1|CI314004
EST:     ACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCCCAGATATG
genomic: ACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88907984|gb|CI090580.1|CI090580
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|86477377|gb|CI120010.1|CI120010
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|29665115|gb|CB661390.1|CB661390
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88510117|gb|CI437623.1|CI437623
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|86869068|gb|CI335635.1|CI335635
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88479955|gb|CI417226.1|CI417226
EST:     TCACATTAGGAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88507520|gb|CI435026.1|CI435026
EST:     ACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: ACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|29674288|gb|CB670563.1|CB670563
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88508926|gb|CI436432.1|CI436432
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCCCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAGGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88470238|gb|CI407509.1|CI407509
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|86851191|gb|CI312592.1|CI312592
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88489221|gb|CI426493.1|CI426493
EST:     GGTCCCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGGTAAGGCATACTTTGCAAAGGAAATCGCAGATATG
genomic: GGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88515234|gb|CI442888.1|CI442888
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88439527|gb|CI551761.1|CI551761
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88516238|gb|CI443892.1|CI443892
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88482794|gb|CI420065.1|CI420065
EST:     AACCTTTCACATTAGGAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCGAAAGAAATCGCAGATATG
genomic: AACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|86841829|gb|CI337476.1|CI337476
EST:     TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATAGCTTTGCAAAAGAAATCGCAGATAT
genomic: TTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATA-CTTTGCAAAAGAAATCGCAGATAT
EST: gi|88483012|gb|CI420283.1|CI420283
EST:     TGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGGTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88906977|gb|CI376049.1|CI376049
EST:     CTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: CTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88474360|gb|CI411631.1|CI411631
EST:     ACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG                         GTCAAAAGACCGCAAGGTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: ACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgt ... acttttgcagGTCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgttaatacaagttggaggagatttctacaccaggtactaattctctatctcaatgacttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC