Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA

Basic information

species Oryza sativa
transcript LOC_Os10g31000.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G150867_T02 (Zea mays), 3'ss of exon 1
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgg---gggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
                                                                                          ||  | |     | |  | ||  | ||  || || | |    ||| |    || |     |||  | | || |  ||  |  |  |   ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| || ||||| || |||||||  ||||
-----------------------------------------------------------------------------------------gtgaggattctggtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G150867_T01 (Zea mays), 3'ss of exon 1
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgg---gggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
                                                                                                      | |  | ||  | ||  || || | |    ||| |    || |     |||  | | || |  ||  |  |  |   ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| || ||||| || |||||||  ||||
-----------------------------------------------------------------------------------------------------gtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AC149818.2_FGT006 (Zea mays), 3'ss of exon 1
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttt---tgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
                                                                                            | ||  |   | |  |  |  | ||  || || | ||   |||   ||||| |     |||  | | || |  ||| |  |  |   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||| || |||||||  ||||
------------------------------------------------------------------------------------------gtgaggattttgtggcgtgtttcggtg-atttttctatgggatttcgatggggattccttgatctgcgtttctactggctgttgatgcctgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA07G07540.2 (Glycine max), 3'ss of exon 1
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
                                                            |||| |          | ||| | ||  | |  |  | |   |  ||||||  | ||| |    |||||    ||    | |   |   |||  | |  | ||  ||| |  ||     ||||||||||| |||||||||||||||||| | || ||||| ||||| ||||| |  ||| | ||||  || || | ||| |
-----------------------------------------------------------gttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaa--gtttgactctt----gattctgattttgatgttagtttttttttttaatta--atagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 1
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
                                                       |||| | ||  |||  ||     |||| ||| ||||   | | || |     |  |||  ||  |   |  ||||  ||||     ||||| |  | || |||  | ||| | |  ||  |  |||||||||||| || ||||||||||||| ||| |||||||| ||||| |||||||| ||||||||||  || || |  || |
----------------------------------------------------gtctgtgatcttttccgaatt-----ttttttttgtattttcgatttc-agaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttgg-attgacatggat-cagGTCAT--CAGGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
                                                        ||| | ||  |||  ||     |||| ||| ||||   | | || |     |  |||  ||  |   |  ||||  ||||     ||||| |  | || |||  | ||| | |  ||  |  |||||||||||| || ||||||||||||| ||| |||||||| ||||| |||||||| ||||||||||  || || |  || |
--------------------------------------------------------gtgatcttttccgaatt-----ttttttttgtattttcgatttc-agaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttgg-attgacatggat-caggtcat--cagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G37650.1 (Glycine max), 3'ss of exon 1
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
                                                       |||| | ||  | |  ||| || | |  |||| |||           || | |      || ||||||  ||| |   |||||||   |  ||||||     |   |  | |  |  |     |||||||||||| || ||||||||||||| | | |||||||| ||||| |||||||| ||||||||||  || || |  || |
----------------------------------------------------gtctgtgatcttttcggaattgtttttgtattttcgatttcataaagtgttcttttgtataaatttgttgtcttttttccatttggggtgtgttggattgaca--tggatcaggtcatcat-----cagGATGATGAGTGATTACAAGGTGGAGACGATCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G03940.2 (Glycine max), 3'ss of exon 1
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctga--tgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
|| |    ||  |   || | | ||  ||||||||              |    ||   |||     |   ||   |  | | |||||||| | ||| || |   |  | ||||   | |||| ||| |||||||||||                   |||| |   |||| |    |   ||||||||||| |||||||||||||||||| | || ||||| ||||| ||||| |  ||| | ||||  || || | ||| |
gttaatccctaatttcttctgttttcctttttttt-------------tttacctttcatttccattcaagtta--taatctttttctatttg-ggtgtctaagtttgactctggattctgtttttgattgttgttttg-------------------ttttttgtttttcctcaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA07G07540.1 (Glycine max), 3'ss of exon 1
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
                                            |    |  |    |  || ||      ||    ||| | |||| |||   | | |   |  | |  ||| ||  | |||  |  |||    |   | |   |   |||  | |  | ||  ||| |  ||     ||||||||||| |||||||||||||||||| | || ||||| ||||| ||||| |  ||| | ||||  || || | ||| |
--------------------------------------------gttaatccaccacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtc-taagtttgactcttgattctgattttgatgttagtttttttttttaatta--atagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgt-----tgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
                                                      |  | |||||   |   ||   |||| ||  | ||||  || | |  | |      || |||   || || | |  |||||    || |    |||| |   ||||  || |   ||| |||     |  ||||||||||| |||||||||||||||||| | || ||||| ||||| |||||||| || |||||| | || || |  || |
-----------------------------------------------------gtaatttttttaatcttatta--tcttatcagtttattcttgattttgagc------tccgat---tttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv15s0046g02280.t01 (Vitis vinifera), 3'ss of exon 1
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctt--tctattggtggtctccatcgtctaatctgatgtgttgttgtt-tgttgttttgggggtggggggattggggattttcttggtttcttgttgttg--cagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
                                                                       ||||||||    ||  ||| ||     | |  ||  | || | |  | | |  || || ||||| ||| | | |    |  ||||   | || ||  |   ||| | |    |||||||||||| || ||||||||||||||| | || ||||| ||||| |||||||  ||| | ||||  || || | ||| |
----------------------------------------------------------------------gttgattctccaattgatcttttcaaaatttt-attttttatttttgtttttaatttttatgttgattttgagctaaaagt-ttggttttcttatttttggtttggtctcaaacagGATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTATGTGCATTTCCATGGACCCAGTGACA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0025g00070.t01 (Vitis vinifera), 3'ss of exon 1
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
                                                                                            ||    |   | ||      ||   | || |||| |||| ||||   |  |     ||| ||| ||||  |  ||   | ||||| |||||||||||| || || ||||||||||||||||| ||||| ||||| |||||||  || || ||||  || ||   ||| |
--------------------------------------------------------------------------------------------gtaagtttttttgt------tgggatttttttgtgtgttttttttaag--gatttaatttgggttttttgtcattgtgttttgttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
                                                   | |||||||| |      | ||  || | || ||   |||||||   |   | |   |||| |    ||||||||| ||   | ||  | |    | ||  | |||     |||            | ||||||||||| ||||||||||| ||||||||||| ||||| |||   || ||||  ||||| || |  || ||   ||| |
---------------------------------------------------ggattgtgttgt------gattacttttcttgttcgaattggtgcggt---ttggggaatc-ggcaagttgttgtt-gt--atctgacgattcaagaatgtgtgat-----tgg------------gtagGATGATGAGTGACTACAAGGTCGAGATGGTGAATGATGGAATGAGCGAATTCTATGTGGAGTTTCATGGACCGCGTGAGA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ23672 (Selaginella moellendorffii), 3'ss of exon 1
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctatt-ggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
                                               |   |  | |  |  |  |    ||  |||| ||  |  || |   ||||     |    |   |||  |   | | | | |     | ||    |     | ||     ||||  |      |  |  || |||||||||||| |||||||||||||||||||| |||||||||||| | |||||    ||||| ||||  || |||   || |
-----------------------------------------------gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggctatgaaaaacctctct--ttcttcgctttcttcctctctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ34378 (Selaginella moellendorffii), 3'ss of exon 1
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
                                                       || || |   | |   | || | |    |   | ||   | ||||||  |     |||  |   | | | | |     | ||    |     | ||     ||||  |      |  |  || |||||||||||| |||||||||||||||||||| |||||||||||| | |||||    ||||| ||||  || |||   || |
------------------------------------------------------gtgagtctcgcctcctctcgaatttcaattccttctt--cgctctccagtggacc-tctctttcttcgctttcttcctctctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

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|163920118|gb|EG709876.1|EG709876
EST:     GTCAAGATGTCTTCCCCGAGCAAGCGCCGCGAGATGGACTTGATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTT
genomic: GTCAAGATGTCTTCCCCGAGCAAGCGCCGCGAGATGGACTTGATGAAGCTgtgaggatct ... gttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTT
EST: gi|58659537|gb|CK048217.1|CK048217
EST:     GTCAAGATGTCTTCCCCGAGCAAGCGCCGCGAGATGGAGTTGATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTT
genomic: GTCAAGATGTCTTCCCCGAGCAAGCGCCGCGAGATGGACTTGATGAAGCTgtgaggatct ... gttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTT
EST: gi|163926790|gb|EG715078.1|EG715078
EST:     GTCAAGATGTCTTCCCCGAGCAAGCGCCGCGAGATGGACTTGATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTT
genomic: GTCAAGATGTCTTCCCCGAGCAAGCGCCGCGAGATGGACTTGATGAAGCTgtgaggatct ... gttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTT
EST: gi|27410240|gb|CA923310.1|CA923310
EST:     CTTGATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTT
genomic: CTTGATGAAGCTgtgaggatct ... gttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTT
EST: gi|163927163|gb|EG715184.1|EG715184
EST:     GTCAAGATGTCTT-CCCGAGCAAGCGCCGCGAGATGGACTTGATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTT
genomic: GTCAAGATGTCTTCCCCGAGCAAGCGCCGCGAGATGGACTTGATGAAGCTgtgaggatct ... gttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTT
EST: gi|86896481|gb|CI328868.1|CI328868
EST:     GTCAAGATGTCTTTCCCGAGCAAGCGCCGCGAGATGGACTTGATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTT
genomic: GTCAAGATGTCTTCCCCGAGCAAGCGCCGCGAGATGGACTTGATGAAGCTgtgaggatct ... gttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTT

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: 75 (upstream exon), 75 (downstream exon)
Score: 86

AGGAGGAGGAGGAGAAAAAGAAATCCAATCTTTTTCTTTTTTCTTCTTGTGTCAAGATGTCTTCCCCGAGCAAGCGCCGCGAGATGGACTTGATGAAGCTgtgaggatct ... gttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
                                       tttcttgtt  CT-rich tract
                             attttctt  TA-rich tract