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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttggatgcttctttacatatgtagcaggaaactataggatgaggaaaaggaactccttgaagttcagtatttctgtttggttgatgcatatttgcagGACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAG

Basic information

species Oryza sativa
transcript LOC_Os02g10480.1
intron # 1
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|88734623|gb|CI758131.1|CI758131
EST:     AAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAG                         GACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
genomic: AAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAGgtaatccaga ... atatttgcagGACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
EST: gi|66928181|gb|CX115029.1|CX115029
EST:     CAAGAACAT-CCTCCCTCCCCTCCCAG-CAGGAGAAATCCAA-                         GACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
genomic: CAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAGgtaatccaga ... atatttgcagGACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
EST: gi|58656726|gb|CK045406.1|CK045406
EST:     TAAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGGCAGGAGAAATCCAAG                         GACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
genomic: TAAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAGgtaatccaga ... atatttgcagGACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
EST: gi|2310113|gb|C26268.1|C26268
EST:     TAAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAG                         GACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
genomic: TAAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAGgtaatccaga ... atatttgcagGACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
EST: gi|88732043|gb|CI757220.1|CI757220
EST:     AAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAG                         GACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
genomic: AAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAGgtaatccaga ... atatttgcagGACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
EST: gi|88388036|gb|CI590312.1|CI590312
EST:     TAAGTCCCAAGAACATCCCTCCCTACCCTCCCAGGCAGGAGAAATCCAAG                         GACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
genomic: TAAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAGgtaatccaga ... atatttgcagGACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
EST: gi|88735087|gb|CI758595.1|CI758595
EST:     AAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAG                         GACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
genomic: AAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAGgtaatccaga ... atatttgcagGACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
EST: gi|88727576|gb|CI751231.1|CI751231
EST:     TAAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAG                         GACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
genomic: TAAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAGgtaatccaga ... atatttgcagGACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
EST: gi|88305672|gb|CI632039.1|CI632039
EST:     TAAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAG                         GACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
genomic: TAAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAGgtaatccaga ... atatttgcagGACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
EST: gi|88385241|gb|CI630342.1|CI630342
EST:     TAAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAG                         GACTGAAAANATTGGAAAGTGTAACTACGCAGTAAGAAGATCTGAATATGA
genomic: TAAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAGgtaatccaga ... atatttgcagGACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
EST: gi|88735299|gb|CI758807.1|CI758807
EST:     AAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAG                         GACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA
genomic: AAGTCCCAAGAACATCCCTCCCTCCCCTCCCAGCCAGGAGAAATCCAAGgtaatccaga ... atatttgcagGACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaaaaggaactccttgaagttcagtatttctgtttggttgatgcatatttgcagGACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAG
                                    ggttgat  putative branch site (score: 5)
                                             atattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttggatgcttctttacatatgtagcaggaaactataggatgaggaaaaggaactccttgaagttcagtatttctgtttggttgatgcatatttgcagGACTGAAAACATTGGAAAGTGTAACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAG

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