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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccattgtccgattcttcgcgtatacactatccctgggacctcactaacctcatggacacacatgcacgctagATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCGCCGGACCTGTTCGCGAGCTATTACGGATGACCAAGCTTCGCCAACCTTT

Basic information

species Oryza sativa
transcript LOC_Os12g42730.4
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|29680089|gb|CB676364.1|CB676364
EST:     GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCG                         ATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
genomic: GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCGgtgagccatt ... tgcacgctagATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
EST: gi|58592088|gb|CF990396.1|CF990396
EST:     GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCG                         ATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
genomic: GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCGgtgagccatt ... tgcacgctagATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
EST: gi|29679033|gb|CB675308.1|CB675308
EST:     GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCG                         ATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
genomic: GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCGgtgagccatt ... tgcacgctagATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
EST: gi|29674623|gb|CB670898.1|CB670898
EST:     GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCG                         ATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
genomic: GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCGgtgagccatt ... tgcacgctagATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
EST: gi|29675652|gb|CB671927.1|CB671927
EST:     GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCG                         ATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
genomic: GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCGgtgagccatt ... tgcacgctagATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
EST: gi|29639895|gb|CB644904.1|CB644904
EST:     GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCG                         ATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
genomic: GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCGgtgagccatt ... tgcacgctagATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
EST: gi|29677656|gb|CB673931.1|CB673931
EST:     GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCG                         ATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGTCG
genomic: GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCGgtgagccatt ... tgcacgctagATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
EST: gi|29679976|gb|CB676251.1|CB676251
EST:     GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCG                         ATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
genomic: GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCGgtgagccatt ... tgcacgctagATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
EST: gi|38478499|gb|CF962632.1|CF962632
EST:     GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCG                         ATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
genomic: GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCGgtgagccatt ... tgcacgctagATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
EST: gi|29680084|gb|CB676359.1|CB676359
EST:     GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCG                         ATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG
genomic: GTCTTCTTCACCTCCGGTCGCCGTCGCCATTGTCGATTCCGCCTCCTCCGgtgagccatt ... tgcacgctagATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgtatacactatccctgggacctcactaacctcatggacacacatgcacgctagATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCGCCGGACCTGTTCGCGAGCTATTACGGATGACCAAGCTTCGCCAACCTTT
                        cactaac  putative branch site (score: 1)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagccattgtccgattcttcgcgtatacactatccctgggacctcactaacctcatggacacacatgcacgctagATCTTGGAGTCTTTTGAGCTGTCGCCGTCAACCCGAAGGAGTTTGCCGCCGCCGGACCTGTTCGCGAGCTATTACGGATGACCAAGCTTCGCCAACCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT