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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taccatattgcctatatataatgcgaacaatgttacagctttcctgaaattagtaaaatctcattccaggaccaaagttactaacctatacttgtcccagGCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGACCTCTTCGAGGAGAAAATCGGGCGCGTCCCGCTCTCCACCTGCGAGTGG

Basic information

species Oryza sativa
transcript LOC_Os06g02130.1
intron # 8
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|86478815|gb|CI121448.1|CI121448
EST:     AATAAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAG                         GCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA
genomic: AATAAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAGgtactattgg ... cttgtcccagGCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA
EST: gi|29622508|gb|CB627519.1|CB627519
EST:     CTTGTGAATAAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAG                         GCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA
genomic: CTTGTGAATAAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAGgtactattgg ... cttgtcccagGCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA
EST: gi|29678897|gb|CB675172.1|CB675172
EST:     CTTGTGAATAAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAG                         GCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA
genomic: CTTGTGAATAAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAGgtactattgg ... cttgtcccagGCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA
EST: gi|29660245|gb|CB656520.1|CB656520
EST:     CTGGTGAATAAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAG                         GCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA
genomic: CTTGTGAATAAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAGgtactattgg ... cttgtcccagGCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA
EST: gi|29664576|gb|CB660851.1|CB660851
EST:     CTTGTGAATAAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAG                         GCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA
genomic: CTTGTGAATAAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAGgtactattgg ... cttgtcccagGCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA
EST: gi|29627697|gb|CB632708.1|CB632708
EST:     CTTGTGAATAAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAG                         GCAACCATGTTTCCGCGACATGCCATTTGTTTTTGTGCTCAACAAGTTCGA
genomic: CTTGTGAATAAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAGgtactattgg ... cttgtcccagGCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA
EST: gi|29622065|gb|CB627076.1|CB627076
EST:     CTTGTGAATAAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAG                         GCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA
genomic: CTTGTGAATAAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAGgtactattgg ... cttgtcccagGCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA
EST: gi|29667762|gb|CB664037.1|CB664037
EST:     AAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAG                         GCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA
genomic: AAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAGgtactattgg ... cttgtcccagGCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA
EST: gi|38478151|gb|CF962284.1|CF962284
EST:     CTTGTGAATAAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAG                         GCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA
genomic: CTTGTGAATAAGATGATCCAAAGCAGGGACTTGTTTGAGGCTACAATCAGgtactattgg ... cttgtcccagGCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaattagtaaaatctcattccaggaccaaagttactaacctatacttgtcccagGCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGACCTCTTCGAGGAGAAAATCGGGCGCGTCCCGCTCTCCACCTGCGAGTGG
                                 tactaac  putative branch site (score: 0)
                                             cttgtccc  putative PPT
     tagtaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taccatattgcctatatataatgcgaacaatgttacagctttcctgaaattagtaaaatctcattccaggaccaaagttactaacctatacttgtcccagGCAACCATGTTTCCGCGACATGCCATTTGTTCTTGTGCTCAACAAGTTCGACCTCTTCGAGGAGAAAATCGGGCGCGTCCCGCTCTCCACCTGCGAGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA