Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttggacatctttgtcgtcaagttgtaactttgtggtatttaccagatgattggctaacttctgatattggaaatcccaaaatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g09320.1
intron # 15
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|29668943|gb|CB665218.1|CB665218
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|218502213|gb|FG961004.1|FG961004
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|29640538|gb|CB645547.1|CB645547
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|218490049|gb|FG963619.1|FG963619
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|29642463|gb|CB647470.1|CB647470
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|218479902|gb|FG948663.1|FG948663
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|218493259|gb|FG949070.1|FG949070
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|58671293|gb|CK059979.1|CK059979
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|29630820|gb|CB635829.1|CB635829
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|29663066|gb|CB659341.1|CB659341
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|58673473|gb|CK062159.1|CK062159
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|58585822|gb|CF984130.1|CF984130
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|29645566|gb|CB650573.1|CB650573
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|29626361|gb|CB631372.1|CB631372
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|87041092|gb|CI195714.1|CI195714
EST:     AAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: AAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|58607251|gb|CK035284.1|CK035284
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|29626362|gb|CB631373.1|CB631373
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|218502862|gb|FG946696.1|FG946696
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|218497744|gb|FG966597.1|FG966597
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
EST: gi|8956808|gb|BE230611.1|BE230611
EST:     GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG                         CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT
genomic: GCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACT

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: 110

TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttgga ... caaaatgcagCGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAGgttagttggacatctttgtcgtcaagttgtaactttgtggtatttaccagatgattggctaacttctgatattggaaatcccaaaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT