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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattcccctcctatatatcgatgatgatttagacgttgatcgacaacattttactaaagtgttatgtttctcttcatccgcagCTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACGGTAATGAAAACTCACACAACATGGGATGGACAGAGACCGACGCTTTCCA

Basic information

species Oryza sativa
transcript LOC_Os08g27030.2
intron # 7
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|86525481|gb|CI165687.1|CI165687
EST:     TGCTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTGATGCTGATG                         CTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACG
genomic: TGCTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTGATGCTGATGgtacattccc ... tcatccgcagCTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACG
EST: gi|88524836|gb|CI453788.1|CI453788
EST:     TGCTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTGATGCTGATG                         CTATATGGCCTCATGGTCACTTCCAACTGGTAGCCGAGTCACGAAGCAACG
genomic: TGCTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTGATGCTGATGgtacattccc ... tcatccgcagCTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACG
EST: gi|58654337|gb|CK043017.1|CK043017
EST:     TGCTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTGATGCTGATG                         CTATATGNCCTCATGCTCACTTCCAACAGCTAGCCGAGTCACGAAGCAACG
genomic: TGCTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTGATGCTGATGgtacattccc ... tcatccgcagCTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACG
EST: gi|86870409|gb|CI320505.1|CI320505
EST:     TGCTTCGTTTTGTTACCTCCAATTTTTCCCATATCCATTTGATGCTTATG                         CTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACG
genomic: TGCTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTGATGCTGATGgtacattccc ... tcatccgcagCTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACG
EST: gi|33654798|gb|CF277412.1|CF277412
EST:     TGCTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTGATGCTGATG                         CTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACG
genomic: TGCTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTGATGCTGATGgtacattccc ... tcatccgcagCTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACG
EST: gi|86838783|gb|CI330238.1|CI330238
EST:     TGCTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTGATGCTGATG                         CTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACG
genomic: TGCTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTGATGCTGATGgtacattccc ... tcatccgcagCTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACG
EST: gi|86833877|gb|CI338248.1|CI338248
EST:     CTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTGATGCTGATG                         CTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACG
genomic: CTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTGATGCTGATGgtacattccc ... tcatccgcagCTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACG
EST: gi|88277407|gb|CI398209.1|CI398209
EST:     ATCCATTTGATGCTGATG                         CTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACG
genomic: ATCCATTTGATGCTGATGgtacattccc ... tcatccgcagCTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagacgttgatcgacaacattttactaaagtgttatgtttctcttcatccgcagCTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACGGTAATGAAAACTCACACAACATGGGATGGACAGAGACCGACGCTTTCCA
                       tactaaa  putative branch site (score: 1)
                                    tgtttctcttcatcc  putative PPT
                aacattttactaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattcccctcctatatatcgatgatgatttagacgttgatcgacaacattttactaaagtgttatgtttctcttcatccgcagCTATATGGCCTCATGCTCACTTCCAACTGCTAGCCGAGTCACGAAGCAACGGTAATGAAAACTCACACAACATGGGATGGACAGAGACCGACGCTTTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA