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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgctgttaaacgattcaatctatattgttctcatccctttattgttactgcgcttactctatgatctatgggctgaattagtgtttatcggcaggcagGACGCAGGACAGAGAATGGGTTTCGAAGAAACATATTTTTCTGCCTTCTGTTACTTGCTTCTTTTCTCTGTCAGCTGGAAATGCCAAGCTGCAGAACTGG

Basic information

species Oryza sativa
transcript LOC_Os11g03780.2
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|88727707|gb|CI749509.1|CI749509
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|88405712|gb|CI609611.1|CI609611
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|88364204|gb|CI610548.1|CI610548
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|88695436|gb|CI737474.1|CI737474
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|88404761|gb|CI583568.1|CI583568
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|58671742|gb|CK060428.1|CK060428
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|88421573|gb|CI618697.1|CI618697
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|88692709|gb|CI736284.1|CI736284
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|88718003|gb|CI741513.1|CI741513
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|88314645|gb|CI606713.1|CI606713
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|88731532|gb|CI755145.1|CI755145
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|88723938|gb|CI745635.1|CI745635
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|88392471|gb|CI612945.1|CI612945
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|88372707|gb|CI612635.1|CI612635
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|88726971|gb|CI750626.1|CI750626
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|88314494|gb|CI604978.1|CI604978
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|88695959|gb|CI739534.1|CI739534
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|428871|gb|D25027.1|D25027
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAG                         GACGCAGGACAGAGAATGGGTTTCGAAGAAACATATTTTTCTGCCTTCTGT
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGgttcaaatct ... cggcaggcagGACGCAGGACAGAGAATGGGTTTCGAAGAAACATATTTTTCTGCCTTCTGT
EST: gi|88311923|gb|CI577529.1|CI577529
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAG                         GACGCAGGACAGAGAATGGGTTTCGAAGAAACATATTTTTCTGCCTTCTGT
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGgttcaaatct ... cggcaggcagGACGCAGGACAGAGAATGGGTTTCGAAGAAACATATTTTTCTGCCTTCTGT
EST: gi|88721230|gb|CI744529.1|CI744529
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg
EST: gi|88719222|gb|CI742732.1|CI742732
EST:     TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGGCAG                      
genomic: TTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCAT----AGgttcaaatct ... cggcagg

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), 15 (downstream exon)
Score: 3

AGCTCTAACACTATCGAAGCTTCACAAATTCAGTTGACGAATTGTAGCTGTTCTCTCTCGTCTCCAAGTGTTGGAGGCAAAGGAATCCTTCGATCCATAGgttcaaatct ... cggcaggcagGACGCAGGACAGAGAATGGGTTTCGAAGAAACATATTTTTCTGCCTTCTGTTACTTGCTTCTTTTCTCTGTCAGCTGGAAATGCCAAGCTGCAGAACTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttactgcgcttactctatgatctatgggctgaattagtgtttatcggcaggcagGACGCAGGACAGAGAATGGGTTTCGAAGAAACATATTTTTCTGCCTTCTGTTACTTGCTTCTTTTCTCTGTCAGCTGGAAATGCCAAGCTGCAGAACTGG
       cgcttac  putative branch site (score: 3)
                              tgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgctgttaaacgattcaatctatattgttctcatccctttattgttactgcgcttactctatgatctatgggctgaattagtgtttatcggcaggcagGACGCAGGACAGAGAATGGGTTTCGAAGAAACATATTTTTCTGCCTTCTGTTACTTGCTTCTTTTCTCTGTCAGCTGGAAATGCCAAGCTGCAGAACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- tgctgtt
- - - - - - - - - - - - - ttgttct
- - - - - - - - - - - - - - - - -catccct
- - - - - - - - - - - - - - - - - - - - - - - ttactgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgaat