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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catcacaaatgttctgctcgtgttagtcagatatgatactgcaaacatcattttatggtttcagctggttggcgcttaattatgatcatgtctactgtagGCTGTCCTGTGGATGCATCTAGACATCAACGTGCAGGCGTTAGGCTTGAAGCAACATTGGGCTAATTCTACCGGAGAAGCCAAATAATATCATATCTAAC

Basic information

species Oryza sativa
transcript LOC_Os03g16110.1
intron # 3
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|88473423|gb|CI410694.1|CI410694
EST:     TAGCGACTCTGAG                         GCTGTCCTGTGAATGCATCTAGACATCAACGTGCAGGCGTTAGGCTTGAAG
genomic: TAGCGACTCTGAGgtcagttgca ... tctactgtagGCTGTCCTGTGGATGCATCTAGACATCAACGTGCAGGCGTTAGGCTTGAAG
EST: gi|487319|gb|D30003.1|D30003
EST:     AAACAAAATGTGAAATGGTGAAGCC-ATTTCCGGTCATAGGG-CTCTTAA                         GCTGCCCTGTGG
genomic: AAACAAAATGTGAAATGGTGAAGCCCATTTC-GCTCATAGCGACTCTGAGgtcagttgca ... tctactgtagGCTGTCCTGTGG
EST: gi|58690664|gb|CK079351.1|CK079351
EST:     CAAACAAAATGTGAAATGGTGAAGCCCATTTCGCTCATAGCGACTCTGAG                         GCTGTCCTGTGGATGCATCTAGACATCAACGTGCAGGCGTTAGGCTTGAAG
genomic: CAAACAAAATGTGAAATGGTGAAGCCCATTTCGCTCATAGCGACTCTGAGgtcagttgca ... tctactgtagGCTGTCCTGTGGATGCATCTAGACATCAACGTGCAGGCGTTAGGCTTGAAG
EST: gi|58587689|gb|CF985997.1|CF985997
EST:     CAAACAAAATGTGAAATGGTGAAGCCCATTTCGCTCATAGCGACTCTGAG                         GCTGTCCTGTGGATGCATCTAGACATCAACGTGC
genomic: CAAACAAAATGTGAAATGGTGAAGCCCATTTCGCTCATAGCGACTCTGAGgtcagttgca ... tctactgtagGCTGTCCTGTGGATGCATCTAGACATCAACGTGC
EST: gi|88831113|gb|CI080537.1|CI080537
EST:     CAAACCAAATGTGAAATGGTGAAGCCCATTTCGCTCATAGCGGCTCTGAG                         GCTGTCCTGTGGATGCATCTAGACATCAACGTGCAGGCGTTAGGCTTGAAG
genomic: CAAACAAAATGTGAAATGGTGAAGCCCATTTCGCTCATAGCGACTCTGAGgtcagttgca ... tctactgtagGCTGTCCTGTGGATGCATCTAGACATCAACGTGCAGGCGTTAGGCTTGAAG
EST: gi|88835114|gb|CI370417.1|CI370417
EST:     CAAACAAAATGTGAAATGGTGAAGCCCATTTCGCTCATAGCGACTCTGAG                         GCTGTCCTGTGGATGCATCTAGACATCAACGTGCAGGCGTTAGGCTTGAAG
genomic: CAAACAAAATGTGAAATGGTGAAGCCCATTTCGCTCATAGCGACTCTGAGgtcagttgca ... tctactgtagGCTGTCCTGTGGATGCATCTAGACATCAACGTGCAGGCGTTAGGCTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcattttatggtttcagctggttggcgcttaattatgatcatgtctactgtagGCTGTCCTGTGGATGCATCTAGACATCAACGTGCAGGCGTTAGGCTTGAAGCAACATTGGGCTAATTCTACCGGAGAAGCCAAATAATATCATATCTAAC
                            gcttaat  putative branch site (score: 4)
                              ttaattatgatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catcacaaatgttctgctcgtgttagtcagatatgatactgcaaacatcattttatggtttcagctggttggcgcttaattatgatcatgtctactgtagGCTGTCCTGTGGATGCATCTAGACATCAACGTGCAGGCGTTAGGCTTGAAGCAACATTGGGCTAATTCTACCGGAGAAGCCAAATAATATCATATCTAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- -cacaaat
- - - - - -ttctgct
- - - - - - - - - - - - - - - - - - tactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggcgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttatgat