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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaacacgttaatcgctacttccctttacaaagtatcattattcatatgcattaatctctattgtgtttgccaacatttttatccttatacagGTTCTAAGATTTCTACTATCCAATGCAAGATGGTGGCTCGAGGAGTATAAGTTTGATGGTTTCAGATTTGACGGTGTAACCTCAATGATGTACACTCATC

Basic information

species Oryza sativa
transcript LOC_Os02g32660.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 12
gtaaggaacacgttaatcgctacttccctttacaaagtatcattattcatatgcattaatctctattgtgtttgccaacatttttatccttatacagGTTCTAAGATTTCTACTATCCAATGCAAGATGGTGGCTCGAGGAGTATAAGTTTGATGGTTTCAGATTTGACGGTGTAACCTCAATGATGTACACTCATC
||| ||||||    |  | |||  ||| ||     | | | |||  || |||   |    || ||| ||     |||||| |||||||| ||| |||||| |||||||||| || |||||||| ||||||||||||||||| |||||||||||||||||| | ||||| ||||| ||||| ||||||||||||||||
gtacggaacaaaa-atgctctatctccatt-----aattttatt-ctcctatttttctgcctgtatcgt----tccaacaattttatccgtatgcagGTTTTAAGATTTCTTCTCTCCAATGCTAGATGGTGGCTCGAGGAATATAAGTTTGATGGTTTCCGTTTTGATGGTGTGACCTCCATGATGTACACTCATC

upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA19G37750.2 (Glycine max), 3'ss of exon 12
gtaaggaacacgttaatcgctacttccctttacaaagtatc-----attattcatatgcattaatctctattgtgtttgccaacatttttatcctta-tacagGTTCTAAGATTTCTACTATCCAATGCAAGATGGTGGCTCGAGGAGTATAAGTTTGATGGTTTCAGATTTGACGGTGTAACCTCAATGATGTACACTCATC
|||||       |    |      | | ||  || ||||||     |  |||  ||| | ||    || |  ||   || |   | ||| || |||| |  |||||||||| | |||||| || |||||| |||||||||| || || || ||||||||||| ||  ||||||| ||||| || |||||||||||||| ||||
gtaagtgctggctc---caaagaattcattggcatagtatctgaaaaaaatttctataccttctgttcaacagtaaatgact-tactttaattcttaatttagGTTCTAAGGTATCTACTTTCGAATGCACGATGGTGGCTGGATGAATACAAGTTTGATGGATTTCGATTTGATGGTGTTACATCAATGATGTACACACATC

upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 12
gtaaggaaca-cgttaatcgctacttccctttacaaagtatcattattcat-atgcattaatctctattgtgtttgccaacatttttatcctta-tacagGTTCTAAGATTTCTACTATCCAATGCAAGATGGTGGCTCGAGGAGTATAAGTTTGATGGTTTCAGATTTGACGGTGTAACCTCAATGATGTACACTCATC
|||||      |   ||    | | |     ||     |  ||  |||     | | ||    || |  ||   || |   | ||| || |||| |  |||||||||| | |||||| || ||| ||||||||||||| || || || ||||||||||| ||  ||||||| ||||| || |||||||||||||||||||
gtaagtgctggctccaaagaattcattggcatagtttctgacaaaattttccgtaccttctgttcaacagtaagtgact-tactttaattcttaatttagGTTCTAAGGTATCTACTCTCGAATTCAAGATGGTGGCTGGATGAATACAAGTTTGATGGATTTCGATTTGATGGTGTTACATCAATGATGTACACTCATC

upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT2G36390.1 (Arabidopsis thaliana), 3'ss of exon 12
-------------------gtaaggaacacgttaatcgctacttccctttacaaagtatcattattcatatgcattaatctctattgtgtttgccaacatttttatcct---tatacagGTTCTAAGATTTCTACTATCCAATGCAAGATGGTGGCTCGAGGAGTATAAGTTTGATGGTTTCAGATTTGACGGTGTAACCTCAATGATGTACACTCATC
                   ||    |   |  || |          | ||  |  ||| |   || |   ||  |   |||      ||| |    || |||    | |   |||  |||| || || | ||| || ||||| || ||||||||||| || || || ||||||||||| ||||||||||| ||||| || || ||||||||||||||||
gtatgtctctttccgtagagttgatattgcaatatttatgggaaagcctt-tagtgtagccccatgctggtggttatgtctggtccttgtgtattgacgtttggtccttgtgtatttagGTGCTTAGGTATCTTCTTTCCAACGCGAGATGGTGGCTGGAAGAATACAAGTTTGATGGGTTCAGATTTGATGGTGTGACTTCCATGATGTACACTCATC

upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaaggaacacgttaatcgctacttccctttacaaagta-tcattattcatatgcattaatctctattgtgtttgccaacattttt--atccttat--acagGTTCTAAGATTTCTACTATCCAATGCAAGATGGTGGCTCGAGGAGTATAAGTTTGATGGTTTCAGATTTGACGGTGTAACCTCAATGATGTACACTCATC
||| | |||   ||  |    | ||   |  | || ||| | |  || ||  | | |||| | ||||    |    ||   | |||  ||| ||    ||||||  || ||| ||| || || |||||| | |||||||| || || || ||||||||||| || |||||||| |||||||||||||||||||| |||||||
gtatgtaactttttcgtga--attttaatcgaaaatgtagtgaacatacaacttccttaagcactatcagttccaacagtctcttttgatcttttctaacagGTATTACGATATCTCCTTTCAAATGCACGGTGGTGGCTAGAAGAATACAAGTTTGATGGATTTAGATTTGATGGTGTAACCTCAATGATGTATACTCATC

upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 3'ss of exon 12
gtaaggaacacgttaatcgctacttccctttacaaagtatcattattcatatgcattaatc-tctattgtgtttgccaacatttttatccttatac-agGTTCTAAGATTTCTACTATCCAATGCAAGATGGTGGCTCGAGGAGTATAAGTTTGATGGTTTCAGATTTGACGGTGTAACCTCAATGATGTACACTCATC
          | || || || |     |   | | ||| |  |      |||||  | ||  | | ||||  | |  |  | || | || || |   |||| || ||||| || || || ||||||||||||||||| || ||||| |||||||| || ||||||||||| ||||| || || ||||||||||| || |
---gtatgtgctttgat-gccaaagttcaagaaatagtgttttgccctttatgctcttattgttttttgttgtagggattaattgtctctttgttttagGTACTGAGATTCCTTCTTTCAAATGCAAGATGGTGGCTAGATGAGTACAAGTTTGACGGGTTCAGATTTGATGGTGTGACTTCCATGATGTACACACACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattcatatgcattaatctctattgtgtttgccaacatttttatccttatacagGTTCTAAGATTTCTACTATCCAATGCAAGATGGTGGCTCGAGGAGTATAAGTTTGATGGTTTCAGATTTGACGGTGTAACCTCAATGATGTACACTCATC
           cattaat  putative branch site (score: 3)
                                      tttttatcctt  putative PPT
                                     atttttatccttata  TA-rich tract