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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttaaaaaataggttcctttttatgttatttggcaccattttcatcattctatttgcactggcatgataaacatactacttcttgcagATATAGGTCAAACCACAAATGAGATCCAAAAAGATATGTCGACCGGTGTGAAAAACAAGAATAGCTTTGGAGAACTTTATTATAAACCTGATCACTGTGT

Basic information

species Oryza sativa
transcript LOC_Os11g26710.1
intron # 1
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|88731677|gb|CI755290.1|CI755290
EST:     GTTTTGCTTGGTTCTTCTGCTGTGCTCTGCCATTCCTGCACAAACAAGAG                         ATATAGGTCAAACCACAAATGAGATCCAAAAAGATATGTCGACCGGTGTGA
genomic: GTTTTGCTTGGTTCTTCTGCTGTGCTCTGCCATTCCTGCACAAACAAGAGgtaatttaaa ... cttcttgcagATATAGGTCAAACCACAAATGAGATCCAAAAAGATATGTCGACCGGTGTGA
EST: gi|88355468|gb|CI679186.1|CI679186
EST:     GTTTTGCTTGGTTCTTCTGCTGTGCTCTGCCATTCCTGCACAAACAAGAG                         ATATAGGTCAAACCACAAATGAGATCCAAAAAGATATGTCGACCGGTGTGA
genomic: GTTTTGCTTGGTTCTTCTGCTGTGCTCTGCCATTCCTGCACAAACAAGAGgtaatttaaa ... cttcttgcagATATAGGTCAAACCACAAATGAGATCCAAAAAGATATGTCGACCGGTGTGA
EST: gi|88587364|gb|CI705104.1|CI705104
EST:     GTTTTGCTTGGTTCTTCTGCTGTGCTCTGCCATTCCTGCACAAACAAGAG                         ATATAGGTCAAACCACAAATGAGATCCAAAAAGATATGTCGACCGGTGTGA
genomic: GTTTTGCTTGGTTCTTCTGCTGTGCTCTGCCATTCCTGCACAAACAAGAGgtaatttaaa ... cttcttgcagATATAGGTCAAACCACAAATGAGATCCAAAAAGATATGTCGACCGGTGTGA
EST: gi|88529016|gb|CI457306.1|CI457306
EST:     GTTTTGCTTGGTTCTTCTGCTGTGCTCTGCCATTCCTGCACAAACAAGAG                         ATATAGGTCAAACCACAAATGAGATCCAAAAAGATATGTCGACCGGTGTGA
genomic: GTTTTGCTTGGTTCTTCTGCTGTGCTCTGCCATTCCTGCACAAACAAGAGgtaatttaaa ... cttcttgcagATATAGGTCAAACCACAAATGAGATCCAAAAAGATATGTCGACCGGTGTGA
EST: gi|88554693|gb|CI484889.1|CI484889
EST:     GTTTTGCTTGGTTCTTCTGCTGTGCTCTGCCATTCCTGCACAAACAAGAG                         ATATAGGTCAAACCACAAATGAGATCCCAAAAGATATGTCGACCGGTGTGA
genomic: GTTTTGCTTGGTTCTTCTGCTGTGCTCTGCCATTCCTGCACAAACAAGAGgtaatttaaa ... cttcttgcagATATAGGTCAAACCACAAATGAGATCCAAAAAGATATGTCGACCGGTGTGA

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: 59 (upstream exon), 52 (downstream exon)
Score: 7

TCTTTCGCAATGGGGAAATGTTTAAGGCCGACCCACCAAGAAGTCATGTTGTTTTGCTTGGTTCTTCTGCTGTGCTCTGCCATTCCTGCACAAACAAGAGgtaatttaaa ... cttcttgcagATATAGGTCAAACCACAAATGAGATCCAAAAAGATATGTCGACCGGTGTGAAAAACAAGAATAGCTTTGGAGAACTTTATTATAAACCTGATCACTGTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccattttcatcattctatttgcactggcatgataaacatactacttcttgcagATATAGGTCAAACCACAAATGAGATCCAAAAAGATATGTCGACCGGTGTGAAAAACAAGAATAGCTTTGGAGAACTTTATTATAAACCTGATCACTGTGT
                                          ctacttctt  CT-rich tract
             attctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttaaaaaataggttcctttttatgttatttggcaccattttcatcattctatttgcactggcatgataaacatactacttcttgcagATATAGGTCAAACCACAAATGAGATCCAAAAAGATATGTCGACCGGTGTGAAAAACAAGAATAGCTTTGGAGAACTTTATTATAAACCTGATCACTGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA