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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaactggccctgaaagaatcactatcattcttcagagaaatgcttaccttgaagtgatgcagcaaatggatcatgaatactctcttcttttgaatgaattctgtgtgatctttgtctggtatttcagGGAAACTCATAGAGTATGATAGGCCATCAAGGCTGATGGAGAATGAGGACTCTGCCTTCTGTAAGCTTGTAGCTGAGTACTGGTCCAACTATAGCTGAAT

Basic information

species Oryza sativa
transcript LOC_Os05g10730.2
intron # 10
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|22306197|gb|BQ907419.1|BQ907419
EST:     CAGGGTTCCCACTGTCACTGACAGTGACATGGTCATGGTTCTTTCATACG                         GGAAACTCATAGAGTATGATAGGCCATCAAGGCTGATGGAGAATGAGGACT
genomic: CAGGGTTCCCACTGTCACTGACAGTGACATGGTCATGGTTCTTTCATACGgtaagcaact ... ggtatttcagGGAAACTCATAGAGTATGATAGGCCATCAAGGCTGATGGAGAATGAGGACT
EST: gi|88905796|gb|CI002134.1|CI002134
EST:     CAGGGTTCCCACTGTCACTGACAGTGACATGGTCATGGTTCTTTCATACG                         GGAAACTCATAGAGTATGATAGGCCATCAAGGCTGATGGAGAATGAGGACT
genomic: CAGGGTTCCCACTGTCACTGACAGTGACATGGTCATGGTTCTTTCATACGgtaagcaact ... ggtatttcagGGAAACTCATAGAGTATGATAGGCCATCAAGGCTGATGGAGAATGAGGACT
EST: gi|88227935|gb|CI227415.1|CI227415
EST:     CAGGGTTCCCACTGTCACTGACAGTGACATGGTCATGGTTCTTTCATACG                         GGAAACTCATAGAGTATGATAGGCCATCAAGGCTGATGGAGAATGAGGACT
genomic: CAGGGTTCCCACTGTCACTGACAGTGACATGGTCATGGTTCTTTCATACGgtaagcaact ... ggtatttcagGGAAACTCATAGAGTATGATAGGCCATCAAGGCTGATGGAGAATGAGGACT
EST: gi|58690372|gb|CK079059.1|CK079059
EST:     CAGGGTTCCCACTGTCACTGACAGTGACATGGTCATGGTTCTTTCATACG                         GGAAACTCATAGAGTATGATAGGCCATCAAGGCTGATGGAGAATGAGGACT
genomic: CAGGGTTCCCACTGTCACTGACAGTGACATGGTCATGGTTCTTTCATACGgtaagcaact ... ggtatttcagGGAAACTCATAGAGTATGATAGGCCATCAAGGCTGATGGAGAATGAGGACT
EST: gi|87015086|gb|CI273484.1|CI273484
EST:     CAGGGTTCCCACTGTCACTGACAGTGACATGGTCATGGTTCTTTCATACG                         GGAAACTCATAGAGTATGATAGGCCATCAAGGCTGATGGAGAATGAGGACT
genomic: CAGGGTTCCCACTGTCACTGACAGTGACATGGTCATGGTTCTTTCATACGgtaagcaact ... ggtatttcagGGAAACTCATAGAGTATGATAGGCCATCAAGGCTGATGGAGAATGAGGACT
EST: gi|29679770|gb|CB676045.1|CB676045
EST:     CAGGGTTCCCACTGTCACTGACAGTGACATGGTCATGGTTCTTTCATACG                         GGAAACTCATAGAGTATGATAGGCCATCAAGGCTGATGGAGAATGAGGACT
genomic: CAGGGTTCCCACTGTCACTGACAGTGACATGGTCATGGTTCTTTCATACGgtaagcaact ... ggtatttcagGGAAACTCATAGAGTATGATAGGCCATCAAGGCTGATGGAGAATGAGGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaatactctcttcttttgaatgaattctgtgtgatctttgtctggtatttcagGGAAACTCATAGAGTATGATAGGCCATCAAGGCTGATGGAGAATGAGGACTCTGCCTTCTGTAAGCTTGTAGCTGAGTACTGGTCCAACTATAGCTGAAT
               ttttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaactggccctgaaagaatcactatcattcttcagagaaatgcttaccttgaagtgatgcagcaaatggatcatgaatactctcttcttttgaatgaattctgtgtgatctttgtctggtatttcagGGAAACTCATAGAGTATGATAGGCCATCAAGGCTGATGGAGAATGAGGACTCTGCCTTCTGTAAGCTTGTAGCTGAGTACTGGTCCAACTATAGCTGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA