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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacataatacttagctgaaaactggagtatttatgttggagcccatctgtaacttgtattttgtacagTCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGGAAACCATGCTTGAAGTCATCAAGTGTTCACG

Basic information

species Oryza sativa
transcript LOC_Os09g24570.1
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|86885641|gb|CI309768.1|CI309768
EST:     CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATT                         TCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
genomic: CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATTgtgagtacat ... ttttgtacagTCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
EST: gi|88422549|gb|CI571531.1|CI571531
EST:     CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATT                         TCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
genomic: CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATTgtgagtacat ... ttttgtacagTCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
EST: gi|88397836|gb|CI583154.1|CI583154
EST:     CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATT                         TCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
genomic: CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATTgtgagtacat ... ttttgtacagTCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
EST: gi|88592426|gb|CI710528.1|CI710528
EST:     CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATT                         TCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
genomic: CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATTgtgagtacat ... ttttgtacagTCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
EST: gi|88430811|gb|CI596925.1|CI596925
EST:     CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATT                         TCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
genomic: CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATTgtgagtacat ... ttttgtacagTCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
EST: gi|88444947|gb|CI696389.1|CI696389
EST:     CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATT                         TCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
genomic: CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATTgtgagtacat ... ttttgtacagTCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
EST: gi|88433774|gb|CI582096.1|CI582096
EST:     CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATT                         TCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
genomic: CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATTgtgagtacat ... ttttgtacagTCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
EST: gi|88315799|gb|CI617272.1|CI617272
EST:     CTAAGCCAATGCATGAGTCTCTTCTGAATGATGCTTTGCGGCGAACAATT                         TCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
genomic: CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATTgtgagtacat ... ttttgtacagTCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
EST: gi|88403849|gb|CI611504.1|CI611504
EST:     CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATT                         TCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG
genomic: CTAAGCCAATGCATGAGTCTCTTCTGAATGAGGCTTTGCGGCGAACAATTgtgagtacat ... ttttgtacagTCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgaaaactggagtatttatgttggagcccatctgtaacttgtattttgtacagTCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGGAAACCATGCTTGAAGTCATCAAGTGTTCACG
                                 ctgtaac  putative branch site (score: 3)
              tatttatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacataatacttagctgaaaactggagtatttatgttggagcccatctgtaacttgtattttgtacagTCAAACGAACAAAAGAGAGAGCTGTGGTCACCATTGCCGTACCAAGGTTGGAAACCATGCTTGAAGTCATCAAGTGTTCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG