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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaaatattcagatgtcatggccaagtactttgatgttctgaaatgaaagctctaacctgttttaagttgttttgacatgatttattatgatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAA

Basic information

species Oryza sativa
transcript LOC_Os01g70520.2
intron # 3
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|29612788|gb|CB617801.1|CB617801
EST:     CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAA                         GATGATTTGAAGCTGATGGTTGACACTAACCTAGAGGCTTATAGATTATCC
genomic: CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAAgtatagctca ... gatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC
EST: gi|29620623|gb|CB625634.1|CB625634
EST:     CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAA                         GATGATTTGAAGCTGATGGTTGACACTAACCTAGAGGCTTATACATTATCC
genomic: CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAAgtatagctca ... gatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC
EST: gi|58678434|gb|CK067121.1|CK067121
EST:     GCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAA                         GATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC
genomic: GCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAAgtatagctca ... gatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC
EST: gi|58587977|gb|CF986285.1|CF986285
EST:     CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAA                         GATGATTTGAAGCTGATGGTTGACACTAACCTAGAGGCTTATAGATTATCC
genomic: CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAAgtatagctca ... gatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC
EST: gi|88313076|gb|CI592360.1|CI592360
EST:     CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAA                         GATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC
genomic: CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAAgtatagctca ... gatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC
EST: gi|29619009|gb|CB624021.1|CB624021
EST:     CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAA                         GATGATTTGAAGCTGATGGTTGACACTAACCTAGAGGCTTATAGATTATCC
genomic: CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAAgtatagctca ... gatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC
EST: gi|88454325|gb|CI569897.1|CI569897
EST:     CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAA                         GATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC
genomic: CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAAgtatagctca ... gatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC
EST: gi|58593808|gb|CF992116.1|CF992116
EST:     CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAA                         GATGATTTGAAGCTGATGGTTGACACTAACCTAGAGGCTTATAGATTATCC
genomic: CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAAgtatagctca ... gatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC
EST: gi|117242417|gb|CT842994.1|CT842994
EST:     CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAA                         GATGATTTGAAGCTGATGGTTGACACTAACCTAGAGGCTTATAGATTATCC
genomic: CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAAgtatagctca ... gatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC
EST: gi|29614528|gb|CB619541.1|CB619541
EST:     CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAA                         GATGATTTGAAGCTGATGGTTGACACTAACCTAGAGGCTTATAGATTATCC
genomic: CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAAgtatagctca ... gatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC
EST: gi|58609911|gb|CK037944.1|CK037944
EST:     CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAA                         GATGATTTGAAGCTGATGGTTGACACTAACCTAGAGGCTTATAGATTATCC
genomic: CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAAgtatagctca ... gatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC
EST: gi|88454346|gb|CI569918.1|CI569918
EST:     CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAA                         GATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC
genomic: CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAAgtatagctca ... gatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC
EST: gi|88420750|gb|CI564586.1|CI564586
EST:     CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAA                         GATGATTTGAAGCTGATGGTTGACACCAACCCTAGAGGCTTATAGATTATC
genomic: CGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAAgtatagctca ... gatggttcagGATGATTTGAAGCTGATGGTTGACACCAACC-TAGAGGCTTATAGATTATC
EST: gi|58689675|gb|CK078362.1|CK078362
EST:     GAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAA                         GATGATTTGAAGCTGATGGTTGACACTAACCTAGAGGCTTATAGATTATCC
genomic: GAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAAgtatagctca ... gatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCC

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), 69 (downstream exon)
Score: 7

GGAAAATGCCGGGCAGAAGCACAGCTGATGTCGCCGCCGACGGGTACCACAAGTACAAAgtatagctca ... gatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaagctctaacctgttttaagttgttttgacatgatttattatgatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAA
                                 atgatttattatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaaatattcagatgtcatggccaagtactttgatgttctgaaatgaaagctctaacctgttttaagttgttttgacatgatttattatgatggttcagGATGATTTGAAGCTGATGGTTGACACCAACCTAGAGGCTTATAGATTATCCATCTCCTGGTCGAGGATTATTCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
-aaaaata
- - - - - - - - -catggcc
- - - - - - - - - - - - - - - -ttgatgt
- - - - - - - - - - - - - - - - - - - - - aaatgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgat