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

gttagggaagttggagcttaataatcttacacaattaatttaacaaatgccttaacatttatccatatgtaacgttctagGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG

Basic information

species Oryza sativa
transcript LOC_Os02g08010.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
------------gttagggaagttggagcttaataat---cttacacaattaatttaacaaatgccttaacatttatccatatgtaacgttctagGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG
             ||||       ||| ||| |||||   |  |||    ||||  |||   || ||||    || |  || | | |  ||||||||||| ||||||||||| || ||||||||||||||||||||||||||||| ||||||||||| ||||||||||| |||||| | |||||||| |||||||
gtttggcctatttttagaatctaaggatcttgataatacgcgcacatgcctaatacaacgt-tgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG

upper sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 27
-------------------gttaggg----aagttggagcttaataatcttacacaattaatttaacaaatgccttaacatttatccatatgtaacgttctagGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG
                    ||| |     || ||    | |    |    |||| |  | || | || ||    | | || | |   |       ||  ||||| || |||||||| ||||| || ||||||||||| || || |||||||| |||||||| ||||| ||||| || |||||| |||| ||||| || || |
gattttggcttcatcttggattaagagataaatttatttcatggagacacaacacgagca-ttcagcagattatctgagatgtgta-gttcactttgtg-tagGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAGCTCACTGTTAATGTAGCTGCTCTTGTAATAAATGTTGTGGCCG

upper sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 28
----------gttagggaagttggagcttaataa------tcttacacaattaatttaacaaatgccttaacatttatccatatgtaacgttct----agGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG
           | |||  || |  |  | |  ||      | |   |    |   | |||   |   ||       ||   ||| | |   | |    |||| ||||||||||| || || || ||||||||||| || || ||||| || ||||||||||| || |||||||| |||||| |||| ||||| || || |
gggttttggcttaaggagagatttatttcaccaagacacgtgtcctatggattgctcaacctgtaatttgtgtaagatttctatttcattctttgtgtagGTTGTCCGCTGGGGCCGCTCTGTATATGCAAATATTCAGAAATTTATCCAGTTCCAGCTTACAGTTAATGTTGCTGCTCTTGTAATAAATGTTGTGGCAG

upper sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 27
-----gttaggg--aagttggagcttaataatcttacacaattaa--tttaacaaatgccttaacat--ttatcca---tatgtaacgttct------agGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG
      ||         |||       ||||  |||     |  |     ||||   || || | |   ||||| |   | ||||    |||      |||| || |||||||| ||||| || ||||||||||| || || |||||||| ||||| || ||||| |||||||| |||||| |||| ||||| || || |
cacggattgatcttggattgagaagagataaatttatttcgtggagacacaacacgagcattcataagattatctaagatgtgtagttctctttgtgtagGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAACTCACTGTTAATGTTGCTGCTCTTGTAATAAATGTAGTGGCAG

upper sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 25
----------gttagggaagttggagcttaataatcttacacaat------taatttaacaaatgccttaacatttatccatatgtaacgttctagGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG
             |   ||  | ||      | |||||  ||| |       |  || |    |  || | || | | |  | | ||   ||| |||| || || ||||| ||||| || ||||| || || || || || || ||||||||||||||||| |||||||| || |||||||||||||| || || |
gttagtctactacatcaaatatagaaacatgtgatcttctacattatccttcatctttatgcttttctaatcaataaactctgtttactcttccagGTTGTTCGTTGGGGCCGTTCTGTGTATGCTAACATTCAGAAATTCATACAATTCCAGCTTACTGTGAATGTTGCCGCACTTATAATCAATGTTGTAGCAG

upper sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 27
-------------------------------------------------------------------------------------------------------------gttagggaagttggagct--taataatcttacacaattaatttaacaaatgccttaacatttatccatatgtaacgttc-tagGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG
                                                                                                               |  ||   |||| |||  |  | |||||    |||||   | |   |    |  |  || ||     | | |      ||||| ||||| |||||||| || || ||||| ||||| |||||||| || || || ||||| || || ||||| || |||||| | ||||||||||| ||||
gtttgtatccttagaaaccaaggattcaaatttcttataaaagaagctcctttttgatactcttctgttgcgtgatacttttggaatttcttttcctcgtaaatgtcctcctttgggctttggggctatttgtgatctttt-taattatcctgaattagatatccattttaataatcgtctcattcctatagGTTGTCCGTTGGGGTCGATCTGTGTATGCGAATATTCAAAAGTTCATCCAGTTTCAGCTCACGGTTAATGTCGCAGCTCTTGTCATCAATGTGGTGGCTG

upper sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 27
-----------------gttaggga----agttggagcttaataatcttacacaatta-atttaacaaatgccttaacatttatccatatgtaacgttctagGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG
                  | | |      | ||| |  ||   | |  | || | ||| |  |     ||     ||  |||||   | | |  | |  ||||| || |||||||| ||||| || ||||||||||| ||||| ||||| || |||||||| ||||| |||||||| |||||||| || ||||| |||||  
ttgccatgtatgcatttatgaagaggcttatttgaaaattcccagtaattcatatttatacctggtgtatatgacaat-tttatttgtttttgccatg-tagGTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAGTTCCAGCTCACTGTTAATGTTGCAGCTCTTATTATAAATGTTGTTGCAT

upper sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
gttagggaagttggagcttaataatcttacacaattaatttaacaaatgccttaacatttatccatatgtaacgttct---agGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG
                                   |||  |||||  |       |   | |  |      |  ||||   |||| || ||||||||||| || || ||||| ||||| || |||||||| || |||||||| |||||||||||||  || ||  |  |||| || || || |
----------------------------------gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG

upper sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 23
gttagggaagttggagcttaataatcttacacaattaatttaacaaatgccttaacatttatccatatgtaacgttct---agGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG
                                   |||  |||||  |       |   | |  |      |  ||||   |||| || ||||||||||| || || ||||| ||||| || |||||||| || |||||||| ||||||||||| |  || ||  |  |||| || || || |
----------------------------------gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTAGTTGCGCTGGTTCTCAACGTCGTGGCCG

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|58675775|gb|CK064462.1|CK064462
EST:     AAAGCTCAGATATAATTATTCTGGATGACAATTTTGCTTCAGTTGTAAAG                         GTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAA
genomic: AAAGCTCAGATATAATTATTCTGGATGACAATTTTGCTTCAGTTGTAAAGgttagggaag ... aacgttctagGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAA
EST: gi|58599514|gb|CK010042.1|CK010042
EST:     AAAGCTCAGATATAATTATTCTGGATGACAATTTTGCTTCAGTTGTAAAG                         GTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAA
genomic: AAAGCTCAGATATAATTATTCTGGATGACAATTTTGCTTCAGTTGTAAAGgttagggaag ... aacgttctagGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAA

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: 63 (upstream exon), 58 (downstream exon)
Score: 21

GCAGACATTGGTCTTGCTATGGGTATCCAAGGAACAGAAGTAGCTAAAGAAAGCTCAGATATAATTATTCTGGATGACAATTTTGCTTCAGTTGTAAAGgttagggaag ... aacgttctagGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttacacaattaatttaacaaatgccttaacatttatccatatgtaacgttctagGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG
                                         atgtaac  putative branch site (score: 21)
     acaattaatttaacaa  TA-rich tract