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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaccaacgttctgatattctattcgtttctatgatgttaattcactctgatattttcgttcctgattagGACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGTAATTGACCACATTTTATTACGACAACTTCTTGAAGATACATATGGGATG

Basic information

species Oryza sativa
transcript LOC_Os01g33684.1
intron # 5
splice site 3'
intron type U2

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|86513442|gb|CI156075.1|CI156075
EST:     GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAG                         GACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
genomic: GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAGgtaaaccaac ... tcctgattagGACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
EST: gi|86521641|gb|CI161847.1|CI161847
EST:     GTTGTCCGAGGCTGAAGGAGTGGTGCGAATGGCATGACATAGAGTATAAG                         GACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
genomic: GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAGgtaaaccaac ... tcctgattagGACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
EST: gi|88221089|gb|CI221045.1|CI221045
EST:     GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGGGTATAAG                         GACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
genomic: GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAGgtaaaccaac ... tcctgattagGACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
EST: gi|88262095|gb|CI365671.1|CI365671
EST:     GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAG                         GACATTCAGGAAAATCCAGAAGATTCATACGGGAAGCTGTGATACTTTTGT
genomic: GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAGgtaaaccaac ... tcctgattagGACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
EST: gi|88464359|gb|CI544820.1|CI544820
EST:     GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAG                         GACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
genomic: GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAGgtaaaccaac ... tcctgattagGACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
EST: gi|88428240|gb|CI562506.1|CI562506
EST:     GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAG                         GACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
genomic: GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAGgtaaaccaac ... tcctgattagGACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
EST: gi|88217276|gb|CI217125.1|CI217125
EST:     GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTAT---                         ---A---AGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
genomic: GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAGgtaaaccaac ... tcctgattagGACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
EST: gi|88513140|gb|CI440646.1|CI440646
EST:     GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAG                         GACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
genomic: GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAGgtaaaccaac ... tcctgattagGACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
EST: gi|88428170|gb|CI557064.1|CI557064
EST:     GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAG                         GACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
genomic: GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAGgtaaaccaac ... tcctgattagGACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
EST: gi|88216717|gb|CI216566.1|CI216566
EST:     GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAG                         GACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
genomic: GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAGgtaaaccaac ... tcctgattagGACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
EST: gi|88269039|gb|CI380337.1|CI380337
EST:     GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAG                         GACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT
genomic: GTTGTCCGAGGCTGAAGAAGTGGTGCGAATGGCATGACATAGAGTATAAGgtaaaccaac ... tcctgattagGACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctattcgtttctatgatgttaattcactctgatattttcgttcctgattagGACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGTAATTGACCACATTTTATTACGACAACTTCTTGAAGATACATATGGGATG
                                      ttttcgttcct  CT-rich tract
                   atgttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaccaacgttctgatattctattcgtttctatgatgttaattcactctgatattttcgttcctgattagGACATTCAGGAAAATCCAGAAGATTCATATGGGAAGCTGTGATACTTTTGTAATTGACCACATTTTATTACGACAACTTCTTGAAGATACATATGGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA