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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcctctttccatcctctttggatcgccgaccacttcaattcacatgcactcgcatacaagagagaattttcttcactgaacctcatgtgtgtgttatcttctttttcattcatcagGTACTTGTCATTTGTCATTGTCAAGGCTACTGACGCATATGAGGCATTGTGTCTGATGCGAAACTTCGTGTCACATGTCTCCATGGACGGTTCAAACATA

Basic information

species Oryza sativa
transcript LOC_Os01g14340.1
intron # 2
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|88958306|gb|CI095825.1|CI095825
EST:     TTCATCAATCCAAGGTTCCAGGAACTGAGGAATGCCACTGCTTTTCCTAATCATCA                    
genomic: TTCATCAATCCAAGGTTCCAGGAACTGAGGAATGCCACTGCTTTTCC---T-A--Agtgagcctct ... cattc
EST: gi|88958306|gb|CI095825.1|CI095825
EST:     TTCATCAATCCAAGGTTCCAGGAACTGAGGAATGCCACTGCTTTTCCTAATCATCA                    
genomic: TTCATCAATCCAAGGTTCCAGGAACTGAGGAATGCCACTGCTTTTCC---T-A--Agtgagcctct ... cattc
EST: gi|88968042|gb|CI098284.1|CI098284
EST:     TTCATCAATCCAAGGTTCCAGGAACTGAGGAATGCCACTGCTTTTCCTAA                         GTACTTGTCATTTGTCATTGTCAAGGCTACTGACGCATATGAGGCATTGTG
genomic: TTCATCAATCCAAGGTTCCAGGAACTGAGGAATGCCACTGCTTTTCCTAAgtgagcctct ... cattcatcagGTACTTGTCATTTGTCATTGTCAAGGCTACTGACGCATATGAGGCATTGTG
EST: gi|88968446|gb|CI098688.1|CI098688
EST:     TTCATCAATCCAAGGTTCCAGGAACTGAGGAATGCCACTGCTTTTCCTAA                         GTACTTGTCATTTGTCATTGTCAAGGCTACTGACGCATATGAGGCATTGTG
genomic: TTCATCAATCCAAGGTTCCAGGAACTGAGGAATGCCACTGCTTTTCCTAAgtgagcctct ... cattcatcagGTACTTGTCATTTGTCATTGTCAAGGCTACTGACGCATATGAGGCATTGTG
EST: gi|86484206|gb|CI126839.1|CI126839
EST:     TTCATCAATCCAAGGTTCCAGGAACTGAGGAATGCCACTGCTTTTCCTAA                         GTACTTGTCATTNGTAATTGTCCAAGGCTACTGACGCATATGAGGCATTGT
genomic: TTCATCAATCCAAGGTTCCAGGAACTGAGGAATGCCACTGCTTTTCCTAAgtgagcctct ... cattcatcagGTACTTGTCATTTGTCATTGTC-AAGGCTACTGACGCATATGAGGCATTGT
EST: gi|88968669|gb|CI098861.1|CI098861
EST:     TTCATCAATCCAAGGTTCCAGGAACTGAGGAATGCCACTGCTTTTCCTAA                         GTACTTGTCATTTGTCATTGTCAAGGCTACTGACGCATATGAGGCATTGTG
genomic: TTCATCAATCCAAGGTTCCAGGAACTGAGGAATGCCACTGCTTTTCCTAAgtgagcctct ... cattcatcagGTACTTGTCATTTGTCATTGTCAAGGCTACTGACGCATATGAGGCATTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaattttcttcactgaacctcatgtgtgtgttatcttctttttcattcatcagGTACTTGTCATTTGTCATTGTCAAGGCTACTGACGCATATGAGGCATTGTGTCTGATGCGAAACTTCGTGTCACATGTCTCCATGGACGGTTCAAACATA
                                ttatcttctttttcat  CT-rich tract
                                        tttttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcctctttccatcctctttggatcgccgaccacttcaattcacatgcactcgcatacaagagagaattttcttcactgaacctcatgtgtgtgttatcttctttttcattcatcagGTACTTGTCATTTGTCATTGTCAAGGCTACTGACGCATATGAGGCATTGTGTCTGATGCGAAACTTCGTGTCACATGTCTCCATGGACGGTTCAAACATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA