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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCCTACTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaagcaaccccatctctgatccgctctactctactctactgttcctccacacaaatccatgtgatggcggatggcctcctcgcgttagttcttgtttgcttcaatttcacgctgtcacacgtacgaggtggcggtgcag

Basic information

species Oryza sativa
transcript LOC_Os05g36270.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g36270.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G322953_T04 (Zea mays), 5'ss of exon 1
CATCCTACTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaagcaaccccatctctgatccgctctactctactctactgttcctccacacaa-atccatgtgatggcggatg-gcctcctcgcgttagttcttgtttgcttcaatttcacgctgtcacacgtacgaggtggcggtgcag
|||||||||||||||||||||||||||||||||||| |||| ||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||| | | | | | | |||| | | || | || ||||| | | | || | ||| | | || || |
------CCTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCGCCGCGGTCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGAGAGACCAACGTCCAGgcaagca----cggcaccaccacacacacactgactcgcccgccccgacgatcaccatccactccgcgcctttcgtgcgtactctgctgaattactgagccccc--------------------------------------
















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|33688486|gb|CF316725.1|CF316725
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GTCCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
EST: gi|88354625|gb|CI678668.1|CI678668
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GTCCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
EST: gi|88434653|gb|CI690933.1|CI690933
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GTCCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
EST: gi|88309089|gb|CI654708.1|CI654708
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GTCCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
EST: gi|88575554|gb|CI669699.1|CI669699
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GTCCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTC
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTC
EST: gi|29670800|gb|CB667075.1|CB667075
EST:     CAACAAGGCCAGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCC                      
genomic: CAACAAGGCC-GGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAA----Cgtccaggcaa ... ggcggtg
EST: gi|29670800|gb|CB667075.1|CB667075
EST:     CAACAAGGCCAGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCC                      
genomic: CAACAAGGCC-GGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAA----Cgtccaggcaa ... ggcggtg
EST: gi|29670800|gb|CB667075.1|CB667075
EST:     CAACAAGGCCAGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCC                      
genomic: CAACAAGGCC-GGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAA----Cgtccaggcaa ... ggcggtg
EST: gi|88575220|gb|CI669365.1|CI669365
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GTCCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAG
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAG
EST: gi|33683625|gb|CF311864.1|CF311864
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GTCCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
EST: gi|88332374|gb|CI656243.1|CI656243
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GTCCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
EST: gi|33679306|gb|CF307545.1|CF307545
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GTCCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
EST: gi|88328095|gb|CI649896.1|CI649896
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GNTCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCA
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTCCA
EST: gi|33686898|gb|CF315137.1|CF315137
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCC                      
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAA----Cgtccaggcaa ... ggcggtg
EST: gi|33686898|gb|CF315137.1|CF315137
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCC                      
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAA----Cgtccaggcaa ... ggcggtg
EST: gi|33686898|gb|CF315137.1|CF315137
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCC                      
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAA----Cgtccaggcaa ... ggcggtg
EST: gi|33693501|gb|CF321740.1|CF321740
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GTCCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
EST: gi|33684972|gb|CF313211.1|CF313211
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GTCCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
EST: gi|29656833|gb|CB653108.1|CB653108
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCC                      
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAA----Cgtccaggcaa ... ggcggtg
EST: gi|29656833|gb|CB653108.1|CB653108
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCC                      
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAA----Cgtccaggcaa ... ggcggtg
EST: gi|29656833|gb|CB653108.1|CB653108
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCC                      
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAA----Cgtccaggcaa ... ggcggtg
EST: gi|88592321|gb|CI710419.1|CI710419
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GTCCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
EST: gi|88329945|gb|CI652332.1|CI652332
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GTCCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
EST: gi|29644325|gb|CB649332.1|CB649332
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCC                      
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAA----Cgtccaggcaa ... ggcggtg
EST: gi|29644325|gb|CB649332.1|CB649332
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCC                      
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAA----Cgtccaggcaa ... ggcggtg
EST: gi|29644325|gb|CB649332.1|CB649332
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCC                      
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAA----Cgtccaggcaa ... ggcggtg
EST: gi|33688998|gb|CF317237.1|CF317237
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GTCCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
EST: gi|86877142|gb|CI311444.1|CI311444
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GTCCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCT
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCT
EST: gi|29663073|gb|CB659348.1|CB659348
EST:     TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAAC                         GTCCAGGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC
genomic: TCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaa ... ggcggtgcagG----G--TGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCCTACTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACgtccaggcaagcaaccccatctctgatccgctctactctactctactgttcctccacacaaatccatgtgatggcggatggcctcctcgcgttagttcttgtttgcttcaatttcacgctgtcacacgtacgaggtggcggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA