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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgctaagtatcacttccacctagtaatatctaataccaaagttattctttgttttttcaacttactctaaattttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCC

Basic information

species Oryza sativa
transcript LOC_Os11g06760.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g06760.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G146472_T02 (Zea mays), 3'ss of exon 4
gttagtgctaagtatcacttccacctagtaatatctaataccaaagttattctt-------tgttttttcaacttact-ctaaattttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCC
||| ||  ||     | ||||  ||| ||| |  ||  ||    | || || ||         |||||| ||  |    ||  | | || || ||||||||| | || |||||||||||||  ||  ||||||||||  |||| ||||| ||||| |||||||||||||||||||||||||||||
gttggtagtagtagcctcttctgccttgtagtg-ctgctattggaatttttattaatgtctcatttttttaatctgtcacttcactgttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC

upper sequence: LOC_Os11g06760.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G050982_T01 (Zea mays), 3'ss of exon 3
gttagtgctaagtatcacttccacctagtaatat--ctaataccaaagttatt----ctttgttttttcaacttactctaaattttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCC
||| ||  ||     | ||||  |||  |||||   ||| |   |   |||||      |  |||||| | ||  | ||  | | ||  | ||||||||| | || |||||||||||||  |   | ||||||||  |||| ||||| ||||| |||||||||||||||||||||||||||||
gttcgtagtagtagcctcttctgccttataatactgctattggaacttttattaatgtctcatttttttatctggcacttgactgttcttccagAGAAGGGTTGGAGGTCTTCATCAGAACAGTGCCACTGAATCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC
















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|88339206|gb|CI633777.1|CI633777
EST:     CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAG                         AGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
genomic: CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAGgttagtgcta ... ttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
EST: gi|88571169|gb|CI662542.1|CI662542
EST:     CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAG                         AGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
genomic: CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAGgttagtgcta ... ttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
EST: gi|218484821|gb|FG946766.1|FG946766
EST:     CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAG                         AGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
genomic: CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAGgttagtgcta ... ttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
EST: gi|56157893|gb|C27653.2|C27653
EST:     CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAG                         AGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
genomic: CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAGgttagtgcta ... ttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
EST: gi|25799906|gb|CA755867.1|CA755867
EST:     CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAG                         AGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
genomic: CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAGgttagtgcta ... ttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
EST: gi|88305212|gb|CI652932.1|CI652932
EST:     CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAG                         AGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
genomic: CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAGgttagtgcta ... ttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
EST: gi|88339833|gb|CI649090.1|CI649090
EST:     CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAG                         AGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
genomic: CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAGgttagtgcta ... ttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
EST: gi|13818900|gb|AB060279.1|AB060279
EST:     CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAG                         AGAAAGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
genomic: CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAGgttagtgcta ... ttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
EST: gi|88309325|gb|CI655333.1|CI655333
EST:     CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAG                         AGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
genomic: CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAGgttagtgcta ... ttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
EST: gi|29677609|gb|CB673884.1|CB673884
EST:     CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAG                         AGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
genomic: CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAGgttagtgcta ... ttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
EST: gi|86897912|gb|CI289086.1|CI289086
EST:     CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAG                         AGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
genomic: CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAGgttagtgcta ... ttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
EST: gi|88338693|gb|CI644150.1|CI644150
EST:     CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAG                         AGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
genomic: CTATGGGAAGAGCCATCAATAAGACAGTCATGGTTGTTGAATTGATCAAGgttagtgcta ... ttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
EST: gi|38474027|gb|CF958159.1|CF958159
EST:     GGTTGTTGAATTGATCAAG                         AGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC
genomic: GGTTGTTGAATTGATCAAGgttagtgcta ... ttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaataccaaagttattctttgttttttcaacttactctaaattttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCC
                                           ttttttgttc  CT-rich tract
             ttattctttgtttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgctaagtatcacttccacctagtaatatctaataccaaagttattctttgttttttcaacttactctaaattttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG