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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccacataaataaacatcacacacaatgctgatcagattttctttcatcatcatcattaattccactttcttctcattgcctgaaaatgaaatcttcagAAGAAGAGCCGGCTCAAGGACCTGACGAGGCCAAGACGGTGTCTGAGGAGGACGAAGCTGAGGGAAGAAGAGGAGATGTCAATACTGCTGGGCTTAATCG

Basic information

species Oryza sativa
transcript LOC_Os01g03870.1
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|58612174|gb|CK039886.1|CK039886
EST:     GCTCCATGGATCAGACTCTGGTCATCACCCTCAAGAAGGCCAACAAGAAA                         AAGAAGAGCCGGCTCAAGGACCTGACGAGGCCAAGACGGTGTCTGAGGAGG
genomic: GCTCCATGGATCAGACTCTGGTCATCACCCTCAAGAAGGCCAACAAGAAAgtgagccaca ... aaatcttcagAAGAAGAGCCGGCTCAAGGACCTGACGAGGCCAAGACGGTGTCTGAGGAGG
EST: gi|86505743|gb|CI148376.1|CI148376
EST:     GCTCCATGGATCAGACTCTGGTCATCACCCTCAAGAAGGCCAACAAGAAA                         AAGAAGAGCCGGCTCAAGGACCTGACGAGGCCCAAGACGGTGTCTGAGGAG
genomic: GCTCCATGGATCAGACTCTGGTCATCACCCTCAAGAAGGCCAACAAGAAAgtgagccaca ... aaatcttcagAAGAAGAGCCGGCTCAAGGACCTGACGAGG-CCAAGACGGTGTCTGAGGAG
EST: gi|58595238|gb|CF993546.1|CF993546
EST:     GCTCCATGGATCAGACTCTGGTCATCACCCTCAAGAAGGCCAACAAGAAA                         AAGAAGAGCCGGCTCAAGGACCTGACGAGGCCAAGACGGTGTCTGAGGAGG
genomic: GCTCCATGGATCAGACTCTGGTCATCACCCTCAAGAAGGCCAACAAGAAAgtgagccaca ... aaatcttcagAAGAAGAGCCGGCTCAAGGACCTGACGAGGCCAAGACGGTGTCTGAGGAGG
EST: gi|88850402|gb|CI093083.1|CI093083
EST:     AGACTCTGGTCATCACCCTCAAGAAGGCCAACAAGAAA                         AAGAAGAGCCGGCTCAAGGACCTGACGAGGCCAAGACGGTGTCTGAGGAGG
genomic: AGACTCTGGTCATCACCCTCAAGAAGGCCAACAAGAAAgtgagccaca ... aaatcttcagAAGAAGAGCCGGCTCAAGGACCTGACGAGGCCAAGACGGTGTCTGAGGAGG
EST: gi|88955747|gb|CI092036.1|CI092036
EST:     GCTCCATGGATCAGACTCTGGTCATCACCCTCAAGAAGGCCAACAAGAAA                         AAGAAGAGCCGGCTCAAGGACCTGACGAGGCCAAGACGGTGTCTGAGGAGG
genomic: GCTCCATGGATCAGACTCTGGTCATCACCCTCAAGAAGGCCAACAAGAAAgtgagccaca ... aaatcttcagAAGAAGAGCCGGCTCAAGGACCTGACGAGGCCAAGACGGTGTCTGAGGAGG
EST: gi|86505945|gb|CI148578.1|CI148578
EST:     GCTCCATGGATCAGACTCTGGTCATCACCCTCAAGAAGGCCAACAAGAAA                         AAGAAGAGCCGGCTCAAGGACCTGACGAGGCCAAGACGGTGTCTGAGGAGG
genomic: GCTCCATGGATCAGACTCTGGTCATCACCCTCAAGAAGGCCAACAAGAAAgtgagccaca ... aaatcttcagAAGAAGAGCCGGCTCAAGGACCTGACGAGGCCAAGACGGTGTCTGAGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcatcatcattaattccactttcttctcattgcctgaaaatgaaatcttcagAAGAAGAGCCGGCTCAAGGACCTGACGAGGCCAAGACGGTGTCTGAGGAGGACGAAGCTGAGGGAAGAAGAGGAGATGTCAATACTGCTGGGCTTAATCG
          cattaat  putative branch site (score: 3)
                                                tcttc  putative PPT
        atcattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagccacataaataaacatcacacacaatgctgatcagattttctttcatcatcatcattaattccactttcttctcattgcctgaaaatgaaatcttcagAAGAAGAGCCGGCTCAAGGACCTGACGAGGCCAAGACGGTGTCTGAGGAGGACGAAGCTGAGGGAAGAAGAGGAGATGTCAATACTGCTGGGCTTAATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG