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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTTCTATGTTGGTGATGCCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtggagctgccccttgagcagtccatgaacatttatttgcccagttcacaatagacaatttcaacatgaattttagggtccttagcaggtattg...

Basic information

species Oryza sativa
transcript LOC_Os01g53560.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g53560.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G111510_T01 (Zea mays), 5'ss of exon 14
ATCTTTCTATGTTGGTGATGCCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtggagctgcc--ccttgagcagtccatgaacatttatttgcccagttcacaatagacaatttcaacatgaattttagggtccttagcaggtattg----
|||||||||||| |||||||| |||||||||||||| ||||||||||| ||||||| |||||| ||||||||||         ||    |||  || | ||    | | ||| | | |   |    |||   |||| ||  | | |  | ||  |  |  |||  |  |||     
ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaatcttgtttgcctgtagtaatcagcaagcttttttctccattggattcaa---acaaattgga-aggcctcttgcg--ctatagttgtaattcagag
















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|88851382|gb|CI404434.1|CI404434
EST:     CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAG                         GCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
genomic: CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtgg ... tcaattgcagGCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
EST: gi|88464861|gb|CI512166.1|CI512166
EST:     CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAG                         GCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
genomic: CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtgg ... tcaattgcagGCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
EST: gi|88568175|gb|CI498892.1|CI498892
EST:     GTGATGCAGATAAAGAATTCGCTAAG                         GCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
genomic: GTGATGCAGATAAAGAATTCGCTAAGgtattggtgg ... tcaattgcagGCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
EST: gi|88567111|gb|CI497828.1|CI497828
EST:     TGATCATAGTGATGCAGATAAAGAATTCGCTAAG                         GCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
genomic: TGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtgg ... tcaattgcagGCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
EST: gi|88318392|gb|CI503462.1|CI503462
EST:     CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAG                         GCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
genomic: CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtgg ... tcaattgcagGCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
EST: gi|88293786|gb|CI507895.1|CI507895
EST:     GAATGATCATAGTGATGCAGATAAAGAATTCGCTAAG                         GCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
genomic: GAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtgg ... tcaattgcagGCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
EST: gi|88318344|gb|CI503414.1|CI503414
EST:     CGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAG                         GCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
genomic: CGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtgg ... tcaattgcagGCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
EST: gi|86505425|gb|CI148058.1|CI148058
EST:     CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAG                         GCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
genomic: CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtgg ... tcaattgcagGCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
EST: gi|88508913|gb|CI436419.1|CI436419
EST:     CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAG                         GCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
genomic: CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtgg ... tcaattgcagGCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
EST: gi|88564086|gb|CI494803.1|CI494803
EST:     CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAG                         GCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
genomic: CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtgg ... tcaattgcagGCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
EST: gi|88516737|gb|CI442393.1|CI442393
EST:     CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAG                         GCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
genomic: CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtgg ... tcaattgcagGCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
EST: gi|88287026|gb|CI500086.1|CI500086
EST:     CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAG                         GCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
genomic: CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtgg ... tcaattgcagGCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
EST: gi|88677082|gb|CI731195.1|CI731195
EST:     CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAG                         GCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
genomic: CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtgg ... tcaattgcagGCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
EST: gi|88669236|gb|CI719374.1|CI719374
EST:     CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAG                         GCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
genomic: CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtgg ... tcaattgcagGCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
EST: gi|86433513|gb|CI093856.1|CI093856
EST:     CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAG                         GCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA
genomic: CCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtgg ... tcaattgcagGCCATTGGTCTGAAGTTTCACGTTCCTGAAGAATACTTTGGCGAAGCTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTTTCTATGTTGGTGATGCCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtggagctgccccttgagcagtccatgaacatttatttgcccagttcacaatagacaatttcaacatgaattttagggtccttagcaggtattg

- - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcccc