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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatttatagaaataacacaatctcctatttattggtggataacatgttcagagtctagtgtgcatgtactgctagccagtcttctacctagtgttttagctaacatcagaaaattgcagagcttccttattctttttctttctcctggtggtaatcttttgatgtgacttagGAATGGCGCACAAAAATTGCTGGGCATCTTGATTGCTATTGGGGAAGCTGTGGCATATGTGCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACT

Basic information

species Oryza sativa
transcript LOC_Os09g17840.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g17840.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G307252_T01 (Zea mays), 3'ss of exon 2
gtaagtatttatagaaataacacaatctcctatttattggtggataacatgttcagagtctagtg-tgcatgtactg-ctagccagtcttctacctagtgttttagctaacatcagaaaattgcagagcttccttattctttttctttctcctggtg-------gtaatcttttga-----tgtgacttagGAATGGCGCACAAAAATTGCTGGGCATCTTGATTGCTATTGGGGAAGCTGTGGCATATGTGCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACT
                     |     |  |   || |  | || | ||  |||    | || || || |||   ||  || |||  ||| || | |     ||  || ||||  || || |||| |||||  |  || || |||||    ||||||       || ||   | |      | | ||  || ||||| || || || ||||| || ||| | ||||| ||||| ||||| ||||| ||||| || |||||||||||||||||||| |||||||||||||||
-------------------gtaagtgttgttgggtagta-tagacatcaaattctatatgtattggtggatgctttgattatccatccttttatcaa-----ttgactgacatt-gagaactgcaaagctttatggtttttattcttgtatctggtgttttcatgtgattcatagtgtactttttacccagAAATGGTGCGCAGAAGTTGCTTGGTATCCTTATTGCCATTGGAGAAGCCGTGGCGTATGTTCTCTCTGGAATGTATGGCAGTGTGAGCCAACTTGGAACT

upper sequence: LOC_Os09g17840.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G307252_T02 (Zea mays), 3'ss of exon 1
gtaagtatttatagaaataacacaatctcctatttattggtggataacatgttcagagtctagtgtgcatgtactgctagccagtcttctacctagtgttttagctaacatcagaaaattgcagagcttccttattctttttctttctcctggtg-------gtaatcttttga-----tgtgacttagGAATGGCGCACAAAAATTGCTGGGCATCTTGATTGCTATTGGGGAAGCTGTGGCATATGTGCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACT
                                                                                     ||| || | |     ||  || ||||  || || |||| |||||  |  || || |||||    ||||||       || ||   | |      | | ||  || ||||| || || || ||||| || ||| | ||||| ||||| ||||| ||||| ||||| || |||||||||||||||||||| |||||||||||||||
-----------------------------------------------------------------------------------tccttttatcaa-----ttgactgacatt-gagaactgcaaagctttatggtttttattcttgtatctggtgttttcatgtgattcatagtgtactttttacccagAAATGGTGCGCAGAAGTTGCTTGGTATCCTTATTGCCATTGGAGAAGCCGTGGCGTATGTTCTCTCTGGAATGTATGGCAGTGTGAGCCAACTTGGAACT

upper sequence: LOC_Os09g17840.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA12G17950.1 (Glycine max), 3'ss of exon 2
gtaagtatttatagaaataacacaatctcctatttattggtggataacatgttcagagtctagtgtgcatgtactgctagccagtcttctacctagtgttttagctaacatcagaaaattgcagagcttcct-tattctttttctttctcctggtggtaatct--tttgatgtgactta---gGAATGGCGCACAAAAATTGCTGGGCATCTTGATTGCTATTGGGGAAGCTGTGGCATATGTGCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACT
                                                                                   ||  | |  |  |  | | |  |  | | || |  ||        || | ||| |||  | || ||  |||   | |  |  ||| || |    ||   | ||||| ||||| ||  | || ||||||||||| ||| |||| ||||| || |||||||| || |||||||||||||| |||||  | |||||||||   
-----------------------------------------------------------------------------------gttatgtctcacggttgtcaattttcctaaggaggttttgctcagtcatatatgcttccttttcctattggcattgacataatttcatctcctctaccagAAATGGTGCACAGAAGCTACTTGGCATCTTGATAGCTGTTGGTGAAGCAGTTGCATATGTTCTTTCTGGAATGTATGGTAGTGTTGGTCAACTTGGAGTG

upper sequence: LOC_Os09g17840.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv00s2574g00010.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtatttatagaaataacacaatctcctatttattggtggataacatgttcagagtctagtgtgcatgtactgctagccagtcttctacctagtgttttagctaacatcagaaaattgcagagcttccttattctttttctttctcctggtggtaatcttttgatgtgacttagGAATGGCGCACAAAAATTGCTGGGCATCTTGATTGCTATTGGGGAAGCTGTGGCATATGTGCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACT
                                                                        |    || |     |       | | |||| ||||   |    || || |  |  |  | | |||| | | | |       |  | || || |  ||   || |||||||| ||||||||  | ||||||||| |||| ||| |||| |||||||| |||||||| || || ||||||||||||||||| ||||||||||||  |
-----------------------------------------------------------------------caggaataactgaagtagatttcaatttttttgctagtct----aatttccttatgtaacctgttctatatatatacaacaatc-tgattttctc-tgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT

upper sequence: LOC_Os09g17840.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtatttatagaaataacacaatctcctatttattggtggataacatgttcagagtctagtgtgcatgtactgct-agccagtcttctacctagtgttttagctaacatcagaaaattgcagagcttccttattctttttctttctcctggtggtaatcttttgatgtgacttagGAATGGCGCACAAAAATTGCTGGGCATCTTGATTGCTATTGGGGAAGCTGTGGCATATGTGCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACT
                                                                   || | |   || |   ||  ||| |  |  |   ||  ||||  ||      ||    ||| |     |||| | | | |       |  | || || |  ||   || |||||||| ||||||||  | ||||||||| |||| ||| |||| |||||||| |||||||| || || ||||||||||||||||| ||||||||||||  |
-------------------------------------------------------------------caggaataactgaagtagatttcaatttttttgcttgtctaatttcc-----ttatgtagcct----gttctatatatatacaacaatc-tgattttctc-tgcctctcagGAATGGTGCACAAAAGCTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGTGTTAGCCAACTTGGAGTT

upper sequence: LOC_Os09g17840.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv19s0014g01020.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtatttatagaaataacacaatctcctatttattggtggataacatgttcagagtctagtgtgcatgtactgctagc-cagtcttctacctagtgttttagctaacatcagaaaattgcagagcttccttattctttttctttctcctggtggtaatcttttgatgtgacttagGAATGGCGCACAAAAATTGCTGGGCATCTTGATTGCTATTGGGGAAGCTGTGGCATATGTGCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACT
                                                                   || | |   |||    ||  ||| |  |    ||||||   |  ||   || || |  |  |  | | |||| | | | |    || |  | || || |  |    || |||||||| ||||||||| | ||||||||| |||| ||| |||| |||||||| |||||||| || || |||||||||||||| || ||||||||||||  |
-------------------------------------------------------------------caggaataactaaagtagatttcaattt----ttttag--gagttc---aatttccttatgtagcctgttctatatatatacaatgatc-tgattttctc-ttcctctcagGAATGGTGCACAAAAACTACTGGGCATCCTGATAGCTGTTGGTGAAGCTGTTGCATATGTTCTCTCAGGAATGTATGGCAGCGTTAGCCAACTTGGAGTT

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: 73 (upstream exon), 74 (downstream exon)
Score: 74

GTATTACCCCAATTGTGACATCTGGAATGGTAATGCAACTTCTAGTGGGATCAAAGATTATTGAAGTTGACAACAGTGTGAGAGAGGACCGTGCACTTCTgtaagtattt ... tgtgacttagGAATGGCGCACAAAAATTGCTGGGCATCTTGATTGCTATTGGGGAAGCTGTGGCATATGTGCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagcttccttattctttttctttctcctggtggtaatcttttgatgtgacttagGAATGGCGCACAAAAATTGCTGGGCATCTTGATTGCTATTGGGGAAGCTGTGGCATATGTGCTGTCTGGAATGTATGGCAGTGTAAGCCAACTTGGAACT
                                       ttttgat  putative branch site (score: 74)
         ttattctttttcttt  TA-rich tract