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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG

Basic information

species Oryza sativa
transcript LOC_Os02g32610.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G059671_T01 (Zea mays), 3'ss of exon 9
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgac-tggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttc-gtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG
                                                || |   |  |||| ||| | ||||||   |  ||| || |  | |  |||||| ||         | ||| | ||    ||| | || | ||||  | | ||||| || |||||||| || ||||| ||||| |||||||| ||||||||||||||||| ||||||||||| ||||||||||| ||||||||||||||||| 
------------------------------------------------tggcaccgctatatacttca-ataaagctgacattggcctttcagttgaaattgaagcaatcgtcgtttaatactct---attgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G059671_T03 (Zea mays), 3'ss of exon 9
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgac-tggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttc-gtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG-
                                                || |   |  |||| ||| | ||||||   |  ||| || |  | |  |||||| ||         | ||| | ||    ||| | || | ||||  | | ||||| || |||||||| || ||||| ||||| |||||||| ||||||||||||||||| ||||||||||| ||||||||||| |||||||||||||||||  
------------------------------------------------tggcaccgctatatacttca-ataaagctgacattggcctttcagttgaaattgaagcaatcgtcgtttaatactct---attgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAG

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 11
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacatatgctttatataaagtaa-aggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG
                   |     | |||||  ||  | | |  |  |   |||   |||   || | | || ||| | | | |   |    ||| ||   | | | |   ||  | ||        | |||||  |  ||| | | ||||||||||| |||||||| ||||| || ||||||||||| || || ||  | ||||| || || ||||| ||  | ||||| || || || || ||||||
------------------gtaaactttcagaaaataaatattattgttt--ttggttctatttattttttgaattaatatgatcattatgatgtcataacctttg-tacccattggttaagt------aatttgt-cattttcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 11
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatca-ttgattttgtgt-accttcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG
                                 | |  | ||| | ||| |      | ||   || | |  |||     ||     | |||| || ||  |        |||| ||   ||   || | | | ||| |  ||| | | |||||||||||||||||||| ||||| || ||||||||||| || || ||  | ||||| || || ||||| ||  | ||||| || || || || ||||||
--------------------------------gtaaactttaagaaaataa------acatcaattgttttcagttctatttattttttgaattaatatgatgtcataacctttgtacccattggttaagtatttgtcattttcatgtgcagGCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG
                                             | |||  |       |   ||| ||  |     | ||       ||        | | |||| ||||| | |   | | ||   |||      ||  ||   ||||||||||| |||||||| |||||||| ||||||||||| || || ||  | |||||||| || |||||  | |||||||| ||||| || || || |||
---------------------------------------------gtatgtttaattccttatgttacatgtatgggtgattacttcctga--------tcttggtgtttcttcacatggaacttt--ctttccaattctctgt-cacagGCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGAGATCTAAAATCTCCAAACTTATTGGTTGACAAAAAATATACAGTCAAG

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 10
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttcgtatc---cagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG
                                                    |     | |  |   | | |  |  | |       ||  | | ||| |  |  || ||  |||| |    | |   |||| | |   ||   | |   ||||| ||||| |||||||| ||||| || ||||||||||| || || || || ||| | ||||| ||||| || |||||||| ||||| ||||| ||||||
----------------------------------------------------tatttttttagtgattgttatttggatgcaccttttaccagctaaaata-acttgttttattatcatttccgtgctttttttttttttttaaaacaaacagGCCAAGGGCATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATCGAGATTTGAAGTCTCCAAACCTTTTGGTTGACAAAAAATACACCGTGAAG

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|88585426|gb|CI703056.1|CI703056
EST:     CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTG                         GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
genomic: CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
EST: gi|33675051|gb|CF303290.1|CF303290
EST:     CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTG                         GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
genomic: CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
EST: gi|29665412|gb|CB661687.1|CB661687
EST:     CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTG                         GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCA
genomic: CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCA
EST: gi|29664339|gb|CB660614.1|CB660614
EST:     CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTG                         GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
genomic: CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
EST: gi|58595275|gb|CF993583.1|CF993583
EST:     CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTG                         GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
genomic: CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG

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: 51 (upstream exon), 72 (downstream exon)
Score: 16

AGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattgtaggtgcttctttataaaaatcattgattttgtgtaccttcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG
                           cattgat  putative branch site (score: 16)
                                        taccttc  putative PPT
             ttctttataaaaatca  TA-rich tract