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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattaatgagcatgcacttctgttttatcgtgacttgaatctctgctgagtacaatttctttctgcagcagTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGATGAAGAGGGAAGTGGTGATGATGAGGGAGAGGAAGAGGAGGATGACCATGACA

Basic information

species Oryza sativa
transcript LOC_Os01g66420.2
intron # 4
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|86433437|gb|CI093780.1|CI093780
EST:     AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTG                         TCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGATGAA
genomic: AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaat ... tctgcagcagTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGATGAA
EST: gi|7134950|gb|AU082754.1|AU082754
EST:     AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGCAG                       
genomic: AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGT---Ggtaaattaat ... tctgcagc
EST: gi|89187194|gb|CI047261.1|CI047261
EST:     TCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTG                         TCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGATGAA
genomic: TCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaat ... tctgcagcagTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGATGAA
EST: gi|218504195|gb|FG956553.1|FG956553
EST:     AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTG                         TCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGATGAA
genomic: AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaat ... tctgcagcagTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGATGAA
EST: gi|38478593|gb|CF962726.1|CF962726
EST:     AGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGGGCGAAAGTGCAG                         TCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGATGA
genomic: AGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGT---Ggtaaattaat ... tctgcagcagTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGATGA
EST: gi|58595326|gb|CF993634.1|CF993634
EST:     AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGCAG                       
genomic: AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGT---Ggtaaattaat ... tctgcagc


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctgttttatcgtgacttgaatctctgctgagtacaatttctttctgcagcagTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGATGAAGAGGGAAGTGGTGATGATGAGGGAGAGGAAGAGGAGGATGACCATGACA
                                       tttctttctgc  CT-rich tract
                                     aatttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattaatgagcatgcacttctgttttatcgtgacttgaatctctgctgagtacaatttctttctgcagcagTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGATGAAGAGGGAAGTGGTGATGATGAGGGAGAGGAAGAGGAGGATGACCATGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG