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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGAAGCTTTTCTGCGACAAGGACTACCCAGACAGGCCACCAACTGTAAAATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacgagaaatttggttcagaattatttctaactcttgtgttcaattatttgattaattaaaacttatcttttggagctaatgtag

Basic information

species Oryza sativa
transcript LOC_Os12g41220.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g41220.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S490_20V6.1 (Physcomitrella patens), 5'ss of exon 4
ACTGAAGCTTTTCTGCGACAAGGACTACCCAGACAGGCCACCAACTGTAAAATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacgagaaatttggttcagaattatttctaactcttgtgttcaattatttgattaattaa--aacttatcttttgg-agctaatgtag----------------------------------
| |||| || |||||||||||||||||||| || | |||||||||||| | ||| || ||  | |||||||||||   ||| ||| | ||||  |||||||||   ||| |      || |   |  ||  | ||     |     ||  | ||| | |    |    | ||  |||  ||| | | | ||||                                   
ATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgta-accaccatgttcatgttgtggctttgatgctcttcttcaccgtctgt-attcgctctcctgttcagctagtctgctggcaaccagtgtaagaagagctaactgtcagtatcatgcatttcgtag
















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|33818255|gb|CF334962.1|CF334962
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|86543648|gb|CI183854.1|CI183854
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|86543908|gb|CI184114.1|CI184114
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|86258363|gb|CI064716.1|CI064716
EST:     ACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: ACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|86533819|gb|CI174025.1|CI174025
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|88217780|gb|CI217629.1|CI217629
EST:     ACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: ACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|88205205|gb|CI205054.1|CI205054
EST:     CAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: CAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|89186841|gb|CI052254.1|CI052254
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|86594483|gb|CI253382.1|CI253382
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|87034223|gb|CI188847.1|CI188847
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|88202676|gb|CI201031.1|CI201031
EST:     AATTTCACTCAAGAATCAACATGACCTGCGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|88248623|gb|CI248472.1|CI248472
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|86829249|gb|CI284932.1|CI284932
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|89171107|gb|CI040384.1|CI040384
EST:     GTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: GTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|88976081|gb|CI024324.1|CI024324
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|88204148|gb|CI203997.1|CI203997
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|86882492|gb|CI327247.1|CI327247
EST:     CCTGTGTAAACCCAGAGAATGGATT-                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: CCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|88215956|gb|CI215805.1|CI215805
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|86832895|gb|CI332501.1|CI332501
EST:     AACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|88481233|gb|CI418504.1|CI418504
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|86510834|gb|CI153467.1|CI153467
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|88219795|gb|CI219355.1|CI219355
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|88205593|gb|CI205442.1|CI205442
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|88258944|gb|CI363237.1|CI363237
EST:     CCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: CCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|218484853|gb|FG952402.1|FG952402
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|58672759|gb|CK061445.1|CK061445
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|86596069|gb|CI266572.1|CI266572
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|86546329|gb|CI186535.1|CI186535
EST:     ACCCAGAGAATGGATTG                         GTTGACCTAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: ACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|88221905|gb|CI221861.1|CI221861
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|86506371|gb|CI149004.1|CI149004
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|15850194|gb|BI798470.1|BI798470
EST:     AATTTCACTCAAGAATC-ACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|58679822|gb|CK068509.1|CK068509
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGAGCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|86510835|gb|CI153468.1|CI153468
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|86543405|gb|CI183611.1|CI183611
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|87025235|gb|CI265800.1|CI265800
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|33815684|gb|CF333693.1|CF333693
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|55414862|gb|CV727238.1|CV727238
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|86428958|gb|CI075639.1|CI075639
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
EST: gi|87036157|gb|CI189604.1|CI189604
EST:     AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTG                         GTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA
genomic: AATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACA

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: 75 (upstream exon), 58 (downstream exon)
Score: 58

ACTGAAGCTTTTCTGCGACAAGGACTACCCAGACAGGCCACCAACTGTAAAATTTCACTCAAGAATCAACATGACCTGTGTAAACCCAGAGAATGGATTGgtatgacacg ... gctaatgtagGTTGACCAAAGGAAGTTCAGCCTGTTGTCAAATTGGCGCCGCGAGTACACAATGGAGGCTATCTTGACCCAACTTAAGAAAGAGATGGCAGCATCACACA




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