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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAAAAGAAACAGGTTACGTTGGCCTGAAGAACCAAGGAGCTACCTGTTACATGAACTCTCTACTACAGACACTATACCATATACCATACTTCAGGAAGgtgtgagatcatgcatcataattcagagcattctagactattgtttccagaactaattgactaacttcattattttacccag

Basic information

species Oryza sativa
transcript LOC_Os11g36470.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA13G16170.1 (Glycine max), 5'ss of exon 5
AAAAAAAGAAACAGGTTACGTTGGCCTGAAGAACCAAGGAGCTACCTGTTACATGAACTCTCTACTACAGACACTATACCATATACCATACTTCAGGAAGgtgtgagatcatgcatcataattcagagcattctagactattgtttcca----gaactaattgactaacttcattattttacccag
||| || || || || || ||||| || ||||||||||||||||| ||||| ||||| |||||||| || ||  | || ||||| || || || || ||||| |   |   |   || || ||           |   |    | ||||     || |||| |       |   |        |||
AAAGAAGGAGACTGGCTATGTTGGGCTTAAGAACCAAGGAGCTACGTGTTATATGAATTCTCTACTCCAAACCTTGTATCATATTCCTTATTTTAGAAAGgt-tagaacggtttgtcttattttgttttgcctgaagttcacttatccattgaaaagtaatgggaagttgttcctggacatttcag

upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA10G23680.1 (Glycine max), 5'ss of exon 1
AAAAAAAGAAACAGGTTACGTTGGCCTGAAGAACCAAGGAGCTACCTGTTACATGAACTCTCTACTACAGACACTATACCATATACCATACTTCAGGAAGgtgtgagatcatgcatcataattcagagcattctagactattgtttccagaactaattgactaacttcattattttacccag
|||||| ||||| ||||| ||||| ||||| || ||||||||||| ||||| ||||| ||||| || || ||| | ||||| ||  | || ||| | |||||     |  | ||||   || |  |     |||  | | || | |   ||| ||  | |   | |  ||| ||||   |||
AAAAAAGGAAACTGGTTATGTTGGACTGAAAAATCAAGGAGCTACATGTTATATGAATTCTCTGCTTCAAACATTGTACCACATTTCTTATTTCCGAAAGgttacccagta-gcatataaactttgtaaggtctt-atttttttataaggaaatagctcatgta-taaatttttttgttcag

upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA20G11300.1 (Glycine max), 5'ss of exon 5
AAAAAAAGAAACAGGTTACGTTGGCCTGAAGAACCAAGGAGCTACCTGTTACATGAACTCTCTACTACAGACACTATACCATATACCATACTTCAGGAAGgtgtgagatcatgcatcataattcagagcattctagactattgtttcca----gaactaattga---ctaacttcattattttac---ccag
 || || || || || || ||||| || ||||||||||||||||||||||| ||||| |||||||| || ||  | |||||||| || || ||||| ||||| |   |   |   || || ||           |   |    | ||||     || |||| |     |   | |   || ||||    |||
CAAGAAGGAGACTGGCTATGTTGGGCTTAAGAACCAAGGAGCTACCTGTTATATGAATTCTCTACTTCAAACCTTGTACCATATTCCTTATTTCAGAAAGgt-tagaactgtttgtcttattttgttttgcctgaagttcacatgtccattgaaaagtaatgggaagtttgttcctggatattacatttcag

upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT5G06600.1 (Arabidopsis thaliana), 5'ss of exon 5
AAAAAAAGAAACAGGTTACGTTGGCCTGAAGAACCAAGGAGCTACCTGTTACATGAACTCTCTACTACAGACACTATACCATATACCATACTTCAGGAAGgtgtgagat---catgcatcataattcagagc-----attctaga-----ctattgtttccagaactaattgactaacttcattattttacccag--
 |||||||| || ||||  ||||| || ||||||||||| || || || |||||||| ||||| ||||||||||||||||| ||||| |||||||| |||||  || ||   | ||  |  |  |||||        |||| |         ||||  |||   ||      ||| | ||    || || |      
TAAAAAAGAGACTGGTTTTGTTGGACTCAAGAACCAAGGTGCAACATGCTACATGAATTCTCTCCTACAGACACTATACCACATACCTTACTTCAGAAAGgtaagatatattcttgttttttccttcagtttgttaaattccatgggttctcattgaatccttgaccggacaactgaattttgcatgttgcttgtag

upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT3G11910.2 (Arabidopsis thaliana), 5'ss of exon 5
AAAAAAAGAAACAGGTTACGTTGGCCTGAAGAACCAAGGAGCTACCTGTTACATGAACTCTCTACTACAGACACTATACCATATACCATACTTCAGGAAGgtgtgagatca--tgcatcataattcagagcattctagactattgtttccagaactaattgactaa----cttcattattttacccag-------------
||||||||| |||||||  ||||| || || |||||||| ||||||||||||||||| ||||| || |||||  ||||||| ||||| ||||| || |||||  ||       |   |  |  ||       | ||  |  ||   |||   || |  | ||  ||     || | || |  |||||              
AAAAAAAGAGACAGGTTTTGTTGGACTAAAAAACCAAGGTGCTACCTGTTACATGAATTCTCTCCTGCAGACTTTATACCACATACCTTACTTTAGAAAGgttggatgcttgttttgttttctttttctatttgcttaatcatgagttcgcaaaattctagagaaagacatttgagtaatgcacccatcctttccttgtag

upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 5'ss of exon 5
AAAAAAAGAAACAGGTTACGTTGGCCTGAAGAACCAAGGAGCTACCTGTTACATGAACTCTCTACTACAGACACTATACCATATACCATACTTCAGGAAGgt-gtgagatcatgcatcataattcagagcattctagactattgtttccagaactaattgactaacttc---attattttacccag
||| || || || ||||| ||||| |||||||||||||||||||||||||||||||| || || || |||||||| |||||||| || |||||||| ||||| | || ||  |   |  |  | |    | |  |  | |  | ||    | |  ||   ||||  ||    | | | |    |||
AAAGAAGGAGACTGGTTATGTTGGACTGAAGAACCAAGGAGCTACCTGTTACATGAATTCCCTTCTTCAGACACTCTACCATATTCCTTACTTCAGAAAGgttgggaaattctcttttttcctcctttacttgtttcattgatattatttgcaagaaagcactacatttggaactgtgtatttcag

upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 5'ss of exon 5
AAAAAAAGAAACAGGTTACGTTGGCCTGAAGAACCAAGGAGCTACCTGTTACATGAACTCTCTACTACAGACACTATACCATATACCATACTTCAGGAAGgtgtgagatcatgcatcataattcagagcattctagactat---tgtttccagaactaattgactaacttcattattttacccag-------------
|||||| ||||| ||||| ||||| || |||||||||||||| || ||||||||||||||||| || || || || || ||||| || ||||| || |||||     | |||   || |  |||       |||    ||    | ||     |  || ||||  |   | |  |||||    |              
AAAAAAGGAAACTGGTTATGTTGGACTTAAGAACCAAGGAGCAACTTGTTACATGAACTCTCTCCTCCAAACTCTCTATCATATTCCCTACTTTAGAAAGgttaataaccattgttcttttttctacattgtctctgttacatgtcttcttgaagatatttgaaaagggtaacaattttttggatcatgttttttcag

upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 5'ss of exon 5
AAAAAAAGAAACAGGTTACGTTGGCCTGAAGAACCAAGGAGCTACCTGTTACATGAACTCTCTACTACAGACACTATACCATATACCATACTTCAGGAAGgtgtgagatcatgcatcataattcagagcattctagactatt-gtttccagaactaattgact--aacttcattattttacccag----------
|||||| || || ||||  ||||| |||||||||||||| ||||| ||||||||||| |||||  |||| || || |||||||| || || ||||| ||||| |  ||  ||     ||  |||  |   ||    | ||||  |||| |  | ||  | |    || | | |||||||   |            
AAAAAAGGAGACTGGTTTTGTTGGACTGAAGAACCAAGGGGCTACTTGTTACATGAATTCTCTCTTACAAACTCTCTACCATATTCCTTATTTCAGAAAGgt-taggagtatcttatatttttcttattgtttattattatttatttcaatgagtatctaaaaggaaataccttattttggactatgtatgtcag

upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 3
AAAAAAAGAAACAGGTTACGTTGGCCTGAAGAACCAAGGAGCTACCTGTTACATGAACTCTCTACTACAGACACTATACCATATACCATACTTCAGGAAGgtgtgagatcatgcatcataattcagagcattctagactattgtttccagaactaattgactaacttcattattttacccag
||| ||||| || || |  || || ||||| |||||||||||||| ||||||||||| |||||  |||||||||| || ||  | ||||  ||| | |||||     | |||       | ||    || || |  ||  || ||         |                           
AAAGAAAGAGACGGGATTTGTAGGTCTGAAAAACCAAGGAGCTACTTGTTACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAGgt----aaccat---ctcgattttcttgctttttttacagttattcgtgttggcag--------------------------

upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ18164 (Selaginella moellendorffii), 5'ss of exon 3
AAAAAAAGAAACAGGTTACGTTGGCCTGAAGAACCAAGGAGCTACCTGTTACATGAACTCTCTACTACAGACACTATACCATATACCATACTTCAGGAAGgtgtgagatcatgcatcataattcagagcattctaga-ctattgtttccagaactaattgactaacttcattattttacccag
||| ||||| || || |  || || ||||| |||||||||||||| ||||||||||| |||||  |||||||||| || ||  | ||||  ||| | |||||     | ||| |   ||  |   |    || || |  ||||  |    | |                              
AAAGAAAGAGACGGGATTTGTAGGTCTGAAAAACCAAGGAGCTACTTGTTACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAGgta----accat-ctcgattttcttgcttgttttacagttattcgtgttggcag-----------------------------

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: 29

AAAAAAAGAAACAGGTTACGTTGGCCTGAAGAACCAAGGAGCTACCTGTTACATGAACTCTCTACTACAGACACTATACCATATACCATACTTCAGGAAGgtgtgagatc ... ttttacccagGCTGTGTATCATATGCCAACCACCGAAAATGATATGCCATCTGGGAGTATTCCGTTGGCATTGCAGAGCCTTTTCTACAAGCTCCAGTATAGTGACAATA




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