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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacaggatgaaatattgtgttccttttccttcttattgagaattatattttccattctctttctacacattttcccttgaaaaaaatgtaacaatatctgagttgtttctcttgcagGTGCTCATATTGGTCCAGAGCCTACAACTGACAGATTTGTTGTTATTACT

Basic information

species Oryza sativa
transcript LOC_Os04g57350.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G065012_T03 (Zea mays), 3'ss of exon 9
gtaaacaggatgaaatattgtgttccttttccttcttattgagaattatattttccattctctttctacacattttcccttgaaaaaaatgtaacaatatctgagttgtttctcttgcagGTGCTCATATTGGTCCAGAGCCTACAACTGACAGATTTGTTGTTATTACT
          ||||| | |    |   |  ||   |  |      || |||       |  ||||  ||| | |||           ||| || || ||||||   |  | ||  |||||| ||||||||||| |||||||||||||| ||||| |||||||| || |||
---------gtgaaacaataacatggatcacccattgttc-----ttgtatcccatcattactttgaacaaacttt-----------aatttaccagtatctgcaatactccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT

upper sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA17G01310.1 (Glycine max), 3'ss of exon 9
gtaaacaggatgaaatattgtgttccttttccttcttattgagaattatattttccattctctttctacacattttcccttgaaaaaaatgtaacaatatctgagttgtttctcttgcagGTGCTCATATTGGTCCAGAGCCTACAACTGACAGATTTGTTGTTATTACT
||        |   | ||  | ||  ||    | |||  ||  ||   |||     |   ||     | | |  || | ||    |  || |  ||   | | |    ||  ||   |||| || || ||||| |||||||||||||||||||||||||||||| | |  
gttggttaatttgtagataatattatttgaaatccttcatgcaaaaagtat-----acaatcgagggatataaattactttattgatcatttgtcaccttttaa----ttcttcacacagGAGCACACATTGGACCAGAGCCTACAACTGACAGATTTGTTGTTGTCATG

upper sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 9
gtaaacaggatgaaatattgtgttccttttccttcttattgagaattatattttccattctctttctacacattttcccttgaaaaaaatgtaacaatatctgagttgtttctcttgcagGTGCTCATATTGGTCCAGAGCCTACAACTGACAGATTTGTTGTTATTACT
         ||  |          |     |      || | | ||| |   |  ||    |||  ||   | | |   ||    ||  | |   ||| ||| |    | || ||   ||| ||||||||||| |||||||| |||||||| || ||||||||| | |  
---------atatatacacacacacacacacacatacatgggggattgt---tcaca----cttattatgaaatgtatgttattgaattttttctaat-tctaatgaatgtcact---agGAGCTCATATTGGACCAGAGCCAACAACTGATAGGTTTGTTGTTGTCATG

upper sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA07G39450.1 (Glycine max), 3'ss of exon 9
gtaaacaggatgaaatattgtgttccttttccttcttattgagaattatattttc--------cattctctttctacacattttcccttgaaaaaaatgtaacaatatctgagttgtttctcttgcagGTGCTCATATTGGTCCAGAGCCTACAACTGACAGATTTGTTGTTATTACT
||        |   | ||  ||| ||   | | |  ||||   ||| ||   | |         |   ||     | |||  || | || |  |  || |  ||   | | |    ||  ||   |||| || || ||||| |||||||||||||||||||||||||||||| | |  
gttggttaatttttagataatgtaccagatgcat--tatttgaaatcattcatgcaaaaagtataggatcgagggatacaagttactttaatgatcatttgtcaccttttaa----ttcttcacacagGAGCACACATTGGACCAGAGCCTACAACTGACAGATTTGTTGTTGTCATG

upper sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 9
-------gtaaacaggatgaaatattgtgttccttttccttcttattgagaatt-atattttccattctctttctacacatt-----ttcccttgaaaaaaatgtaacaatatctgagttgt--ttctcttgcagGTGCTCATATTGGTCCAGAGCCTACAACTGACAGATTTGTTGTTATTACT
        |  |    ||   || || |  ||||| |    | ||   ||  |  |||||||  |   | |    |||  |      ||  |   |||| |   | | |  |  | | ||||  |  | || |||| ||||||||||| |||||||| || |||||||||||||||||| | |  
gcaagttatccatcttatcctatcttcttctccttctgtgacctaactagtttcgatattttaaaaagtatgggaacaggtcaatgattaaccgtaaaacagctttatataacttcaattgtcatattttttcagGAGCTCATATTGGACCAGAGCCGACTACTGACAGATTTGTTGTTGTCATG

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), 50 (downstream exon)
Score: 56

AGCAGTGATTTCGATGCGAAGCCAATGGTCATGTTGCTGGGTCAGTATTCCACAGGAAAAACCACATTCATAAAGCATTTACTGAAGACAAATTATCCAGgtaaacagga ... tctcttgcagGTGCTCATATTGGTCCAGAGCCTACAACTGACAGATTTGTTGTTATTACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacacattttcccttgaaaaaaatgtaacaatatctgagttgtttctcttgcagGTGCTCATATTGGTCCAGAGCCTACAACTGACAGATTTGTTGTTATTACT
                       atgtaac  putative branch site (score: 56)
                                        ttgtttctctt  putative PPT
              ttgaaaaaaatgtaac  TA-rich tract