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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctattccccttcctggttgtttgcactgcaatactctcagtggttacattaacatgctatgcttatatggccttttggatgtcattgaactactg...

Basic information

species Oryza sativa
transcript LOC_Os01g47340.1
intron # 2
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|86256613|gb|CI061376.1|CI061376
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|30227110|gb|CB965002.1|CB965002
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|88211340|gb|CI210980.1|CI210980
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|4880543|gb|AU064842.1|AU064842
EST:     ATGGGTAAAAGGGCAAGCAAATGGAGGAAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACNTGTCACTTCCACCAGTAAAGCTCCANTGTAGCAT
genomic: ATGGGT-AAAGGGCAAGCAAATGGAGG-AAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|29624268|gb|CB629279.1|CB629279
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|38473537|gb|CF957669.1|CF957669
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|88440077|gb|CI543994.1|CI543994
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|5004694|gb|AU069925.1|AU069925
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|86254630|gb|CI059357.1|CI059357
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|27577968|gb|CB000663.1|CB000663
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|86848825|gb|CI295663.1|CI295663
EST:     ATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: ATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|218500142|gb|FG957698.1|FG957698
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|29628493|gb|CB633504.1|CB633504
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|58586327|gb|CF984635.1|CF984635
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCAC
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCAC
EST: gi|86593560|gb|CI264439.1|CI264439
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|27576101|gb|CA998795.1|CA998795
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|88210366|gb|CI210215.1|CI210215
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|88974703|gb|CI022999.1|CI022999
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|88367069|gb|CI561631.1|CI561631
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|38478268|gb|CF962401.1|CF962401
EST:     AATGGGTAAAGTGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: AATGGGTAAAG-GGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|29685336|gb|CB681611.1|CB681611
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|88207995|gb|CI207844.1|CI207844
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|29624267|gb|CB629278.1|CB629278
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|12693425|gb|AU173558.1|AU173558
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|58030965|gb|CX728508.1|CX728508
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|163923618|gb|EG715339.1|EG715339
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
EST: gi|218479381|gb|FG952387.1|FG952387
EST:     GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACAC                         TGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT
genomic: GAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCAT

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: 57 (upstream exon), 75 (downstream exon)
Score: 135

CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctatt ... tgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCATGCTTGCTGAGGATGCAATTAAAGCTGCCGTGAAAGACTATGAAGCAAAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACTGAATGGGTAAAGGGCAAGCAAATGGAGGAAGTAGTGACTATAAAAAACACgtaagctattccccttcctggttgtttgcactgcaatactctcagtggttacattaacatgctatgcttatatggccttttggatgtcattgaactactg

- - - - - - - - - - AAGCAA
- - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccttc