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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_Os02g32660.1
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

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: 74 (upstream exon), 75 (downstream exon)
Score: 736

GAACGGTTTTGATGGTACAGATACGCATTACTTTCATAGTGGTTCACGCGGCCATCATTGGATGTGGGATTCTCGCCTTTTCAACTATGGGAATTGGGAAgtaaggaaca ... ccttatacagGTTCTAAGATTTCTACTATCCAATGCAAGATGGTGGCTCGAGGAGTATAAGTTTGATGGTTTCAGATTTGACGGTGTAACCTCAATGATGTACACTCATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattcatatgcattaatctctattgtgtttgccaacatttttatccttatacagGTTCTAAGATTTCTACTATCCAATGCAAGATGGTGGCTCGAGGAGTATAAGTTTGATGGTTTCAGATTTGACGGTGTAACCTCAATGATGTACACTCATC
           cattaat  putative branch site (score: 736)
                                      tttttatcctt  putative PPT
                                     atttttatccttata  TA-rich tract