Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatactaaagtcattatgaagttgaattgagtgctgcattaatattcaataattttcgaagaagaattcaattcttaccatgtttttccttttgcttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAACTTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g47490.2
intron # 4
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|88424671|gb|CI606470.1|CI606470
EST:     GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCT
genomic: GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCT
EST: gi|33681993|gb|CF310232.1|CF310232
EST:     GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
genomic: GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
EST: gi|33681994|gb|CF310233.1|CF310233
EST:     AGGATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAACACCTAAAGGGCCTCTTGAAGCACTTCGAACAAA
genomic: AGGATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAA-ACCTAAAGGGCCTCTTGAAGCACTTCGACCAAA
EST: gi|66915652|gb|CX102500.1|CX102500
EST:     GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
genomic: GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
EST: gi|428714|gb|D24866.1|D24866
EST:     GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
genomic: GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
EST: gi|33693174|gb|CF321413.1|CF321413
EST:     AGGATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
genomic: AGGATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
EST: gi|86429462|gb|CI076143.1|CI076143
EST:     TGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
genomic: TGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
EST: gi|88974597|gb|CI022138.1|CI022138
EST:     GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
genomic: GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
EST: gi|33693173|gb|CF321412.1|CF321412
EST:     GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
genomic: GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
EST: gi|33691810|gb|CF320049.1|CF320049
EST:     GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCCTAAAGGGCCTCTTGAAGCACTTCGACCAAA
genomic: GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAA-CCTAAAGGGCCTCTTGAAGCACTTCGACCAAA
EST: gi|33683325|gb|CF311564.1|CF311564
EST:     GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
genomic: GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
EST: gi|8528336|gb|AU093151.1|AU093151
EST:     CTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
genomic: CTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
EST: gi|58688945|gb|CK077632.1|CK077632
EST:     GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
genomic: GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
EST: gi|55827447|gb|AU030657.2|AU030657
EST:     GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAA-CTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
genomic: GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
EST: gi|88410948|gb|CI581312.1|CI581312
EST:     GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
genomic: GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
EST: gi|428444|gb|D24594.1|D24594
EST:     GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
genomic: GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
EST: gi|33691809|gb|CF320048.1|CF320048
EST:     GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
genomic: GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
EST: gi|88335397|gb|CI650362.1|CI650362
EST:     GATCATGATCGGGCTTACTTCGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGAACTT
genomic: GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTT
EST: gi|2312901|gb|C29056.1|C29056
EST:     GCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
genomic: GCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA
EST: gi|3761993|gb|C99241.1|C99241
EST:     CTGATTGGGCTCTAGGCAAN                         CAAGGTGGAAGCCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAA
genomic: CTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAG-CCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAA
EST: gi|88975414|gb|CI023665.1|CI023665
EST:     GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAG                         CAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCCAAA
genomic: GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAA

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: 48 (upstream exon), 60 (downstream exon)
Score: 42

GATCATGATCGGGCTTACTTTGATTCTGCTGATTGGGCTCTAGGCAAGgtaatactaa ... cttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAACTTCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattttcgaagaagaattcaattcttaccatgtttttccttttgcttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAACTTCAG
                      ttcttac  putative branch site (score: 42)
                                 tttttccttttgcttg  putative PPT
               aattcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatactaaagtcattatgaagttgaattgagtgctgcattaatattcaataattttcgaagaagaattcaattcttaccatgtttttccttttgcttgccgcagCAAGGTGGAAGCCACAAACCTAAAGGGCCTCTTGAAGCACTTCGACCAAAACTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC