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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacatgagattcaatctctacccctgttgctcatatacaagccataaaatctcaccctctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGCAATGATGCTGTTGCTTGCAAAGTTTCCCTTCCTCCAATGCGAAGTTTGG

Basic information

species Oryza sativa
transcript LOC_Os06g08730.1
intron # 18
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|89174999|gb|CI041077.1|CI041077
EST:     GAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTG                         CATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
genomic: GAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
EST: gi|88520416|gb|CI448070.1|CI448070
EST:     GAAAGCTCTCCAGGAATGAATAGATAGATAGATATCCCTCGTTTAGTTTG                         CATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
genomic: GAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
EST: gi|88901697|gb|CI001805.1|CI001805
EST:     GAAAGCTCTCCAGGAATACATAGATAGATAGATATCCCTCGTCTAGTTTG                         CATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
genomic: GAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
EST: gi|33795400|gb|CF323570.1|CF323570
EST:     GAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTG                         CATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
genomic: GAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
EST: gi|88476716|gb|CI413987.1|CI413987
EST:     AAATAGATAGATAGATATCCCTCGTCTAGTTTG                         CATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
genomic: AAATAGATAGATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
EST: gi|88411473|gb|CI518997.1|CI518997
EST:     ATAGATATCCCTCGTCTAGTTTG                         CATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
genomic: ATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
EST: gi|88515858|gb|CI443512.1|CI443512
EST:     GGAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTGTAGTTTG                         CATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
genomic: GAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
EST: gi|89178386|gb|CI391565.1|CI391565
EST:     TAGATAGATATCCCTCGTGTAGTTTG                         CATTTGTGTGCCAGGTCCTCCCGCGAAATGGGAAGCCACAGCCAAGCTCGC
genomic: TAGATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC

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: 75 (upstream exon), 69 (downstream exon)
Score: 8

AGCAACCCCGAGCGACTCAAGAATCAAGTCAGAGAGCTTACCTCCCGTGTGAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGCAATGATGCTGTTGCTTGCAAAGTTTCCCTTCCTCCAATGCGAAGTTTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctctacccctgttgctcatatacaagccataaaatctcaccctctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGCAATGATGCTGTTGCTTGCAAAGTTTCCCTTCCTCCAATGCGAAGTTTGG
                                   atctcac  putative branch site (score: 8)
                                    tctcaccctctgtttc  CT-rich tract
                              ataaaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcacatgagattcaatctctacccctgttgctcatatacaagccataaaatctcaccctctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGCAATGATGCTGTTGCTTGCAAAGTTTCCCTTCCTCCAATGCGAAGTTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG