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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgcacactagggtcttgaagaactgcacgagtcattgtattaaaaaacatcaaccatctctcctgttttctgatctctggcatgttttcctttgctagGTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAACTTTGAGCTAATTGTAGTCTCAATGCCAGGTAGATAATTATTTCCGCGC

Basic information

species Oryza sativa
transcript LOC_Os08g08000.1
intron # 9
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|44666060|gb|CR279494.1|CR279494
EST:     CTGTTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAG                         GTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
genomic: CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAGgtatgcctta ... cctttgctagGTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
EST: gi|163928939|gb|EG709767.1|EG709767
EST:     CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAG                         GTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
genomic: CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAGgtatgcctta ... cctttgctagGTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
EST: gi|58679868|gb|CK068555.1|CK068555
EST:     CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAG                         GTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
genomic: CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAGgtatgcctta ... cctttgctagGTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
EST: gi|42592165|gb|CK738651.1|CK738651
EST:     CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAG                         GTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
genomic: CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAGgtatgcctta ... cctttgctagGTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
EST: gi|29682148|gb|CB678423.1|CB678423
EST:     CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAG                         GTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
genomic: CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAGgtatgcctta ... cctttgctagGTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
EST: gi|58663093|gb|CK051779.1|CK051779
EST:     CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAG                         GTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
genomic: CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAGgtatgcctta ... cctttgctagGTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
EST: gi|88320911|gb|CI528063.1|CI528063
EST:     CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAG                         GTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
genomic: CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAGgtatgcctta ... cctttgctagGTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
EST: gi|58591046|gb|CF989354.1|CF989354
EST:     CTGGTAGCTTTTGCAGAAAATTCTTAACCCTTTGTAAAGTTACTGTACAG                         GTGTTCGTGCTGTGGAAG
genomic: CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAGgtatgcctta ... cctttgctagGTGTTCGTGCTGTGGAAG
EST: gi|29644349|gb|CB649356.1|CB649356
EST:     CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAG                         GTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
genomic: CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAGgtatgcctta ... cctttgctagGTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
EST: gi|88994546|gb|CI117698.1|CI117698
EST:     CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAG                         GTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA
genomic: CTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAGgtatgcctta ... cctttgctagGTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAA

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: 54 (upstream exon), 42 (downstream exon)
Score: 10

TGTGTATGCTCATCCTTCAAATTCAGGACCAGGATGATGTTGAAATTAGGCTGGTAGCTTTTGCAGAAAATTCTTACCCCTTTGTAAAGTTACTGTACAGgtatgcctta ... cctttgctagGTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAACTTTGAGCTAATTGTAGTCTCAATGCCAGGTAGATAATTATTTCCGCGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaacatcaaccatctctcctgttttctgatctctggcatgttttcctttgctagGTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAACTTTGAGCTAATTGTAGTCTCAATGCCAGGTAGATAATTATTTCCGCGC
                        ttctgat  putative branch site (score: 10)
                                       tgttttcctttgct  putative PPT
                                      atgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgcacactagggtcttgaagaactgcacgagtcattgtattaaaaaacatcaaccatctctcctgttttctgatctctggcatgttttcctttgctagGTGTTCGTGCTGTGGAAGCGGCGCGGGTAGCGGTTTCTTCATTTCCCCAAACTTTGAGCTAATTGTAGTCTCAATGCCAGGTAGATAATTATTTCCGCGC

tatgcac
- - - - - - - tcttgaa
- - - - - - - - - - - aactgca
- - - - - - - - - - - - - - - - - - - - - taaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcatgt