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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGCTGCTGCTGCTCCTGCTGCCGGTGGTGCTGGTGGTGCTCCTGCAGCTGAGGCGAAGAAAGAAGATAAGGTCGAAGAGAAGGAAGAAAGTGATGATgtaagaccaatgttcttatttgtctcaattagcatattttgctcattcattatgtctatggtagtttgacatgacttctattcaatgtataatatcgtat...

Basic information

species Oryza sativa
transcript LOC_Os01g09510.1
intron # 3
splice site 5'
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|4714051|gb|AU058018.1|AU058018
EST:     CGAAGAGAAGGAAGAAAGTGATGAT                         GACATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCA
genomic: CGAAGAGAAGGAAGAAAGTGATGATgtaagaccaa ... ttatttacagGACATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCA
EST: gi|3760653|gb|C97907.1|C97907
EST:     CTGAGGCGAAGAANGAAGATAAGGTCGAAGAGAAGGAAGAAAGTGATGAT                         GNCATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCA
genomic: CTGAGGCGAAGAAAGAAGATAAGGTCGAAGAGAAGGAAGAAAGTGATGATgtaagaccaa ... ttatttacagGACATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCA
EST: gi|86855151|gb|CI263218.1|CI263218
EST:     CTGAGGCGAAGAAAGAAGATAAGGTCGAAGAGAAGGAAGAAAGTGATGAT                         GACATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCA
genomic: CTGAGGCGAAGAAAGAAGATAAGGTCGAAGAGAAGGAAGAAAGTGATGATgtaagaccaa ... ttatttacagGACATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCA
EST: gi|88995211|gb|CI036786.1|CI036786
EST:     TGAGGCGAAGAAAGAAGATAAGGTCGAAGAGAAGGAAGAAAGTGATGAT                         GACATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCA
genomic: TGAGGCGAAGAAAGAAGATAAGGTCGAAGAGAAGGAAGAAAGTGATGATgtaagaccaa ... ttatttacagGACATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCA
EST: gi|33810146|gb|CF330962.1|CF330962
EST:     CTGAGGCGAAGAAAGAAGATAAGGTCGAAGAGAAGGAAGAAAGTGATGAT                         GACATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCA
genomic: CTGAGGCGAAGAAAGAAGATAAGGTCGAAGAGAAGGAAGAAAGTGATGATgtaagaccaa ... ttatttacagGACATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCA
EST: gi|88446889|gb|CI528932.1|CI528932
EST:     CTGAGGCGAAGAAAGAAGATAAGGTCGAAGAGAAGGAAGAAAGTGATGAT                         GACATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCA
genomic: CTGAGGCGAAGAAAGAAGATAAGGTCGAAGAGAAGGAAGAAAGTGATGATgtaagaccaa ... ttatttacagGACATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCA
EST: gi|86534426|gb|CI174632.1|CI174632
EST:     CTGAGGCGAAGAAAGAAGATAAGGTCGAAGAGAAGGAAGAAAGTGATGAT                         GACATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCA
genomic: CTGAGGCGAAGAAAGAAGATAAGGTCGAAGAGAAGGAAGAAAGTGATGATgtaagaccaa ... ttatttacagGACATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCA
EST: gi|425968|gb|D22650.1|D22650
EST:     TGAGGCGAAGAAAGAAGATTAAGGTCGAAGAGAAGGAAGAAAGTGATGAT                         GACATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCA
genomic: TGAGGCGAAGAAAGAAGA-TAAGGTCGAAGAGAAGGAAGAAAGTGATGATgtaagaccaa ... ttatttacagGACATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 75 (downstream exon)
Score: 352

TGTTGCTGCTGCTGCTCCTGCTGCCGGTGGTGCTGGTGGTGCTCCTGCAGCTGAGGCGAAGAAAGAAGATAAGGTCGAAGAGAAGGAAGAAAGTGATGATgtaagaccaa ... ttatttacagGACATGGGCTTCAGTTTGTTTGACTGAGTGATGCGGTCACCTCTTCTATCATCAATACCAGACTTTGCGCAGGAAACTAGAGTGATGATGTTTGGGATTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGCTGCTGCTGCTCCTGCTGCCGGTGGTGCTGGTGGTGCTCCTGCAGCTGAGGCGAAGAAAGAAGATAAGGTCGAAGAGAAGGAAGAAAGTGATGATgtaagaccaatgttcttatttgtctcaattagcatattttgctcattcattatgtctatggtagtttgacatgacttctattcaatgtataatatcgtat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA