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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAGgtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtctatttacaccattattgaacag

Basic information

species Oryza sativa
transcript LOC_Os11g01380.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 16
CATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAGgtttgttatcttaagttatgct-ttgttgcctgtctattattactggctggggtggtctatttacaccattattgaacag
|||||  |||| || || ||||||||||||||||| || ||||| |||||||||||||| |||||||||  | || ||||||| | |||     | ||| || ||           | || |||| ||| | |  ||| ||||
CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtgttcagttatgttcttgaaatgtatctgttgttttc--------ttgtttattaacaacttccttgcacag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA14G06340.2 (Glycine max), 5'ss of exon 18
CATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAGgtttgt----tatcttaagtt--atgctttgttgcctgtctattattactggctggggtggtctatttacaccattattgaacag-------------
|||||||||||||||||||| ||||| || || || || ||||| ||||| ||||| || ||||||| |    | |  |   ||  ||   ||   |  |    ||||  ||    |  | ||  || || | |    || | |  |              
CATTACACAGAATTACCAGACATCAAACGCGTGATTGTTAATACACATGCAATTGAACCTCAGgtttatgtgctgttctgcttttaatctcttagagtttaaaaattaaaacccattctg-tgagcttttaaaatacctactcattatgtggttgttacag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 18
CATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAGgtttgttatcttaagttatgctttgttgcctg--tctattattactggctggggtggtctatttacaccattattgaacag
|||||  | ||||| || || ||||| |||||||| |||||||| |||||||| || |||||||||||     | ||||   |||    || |||  |||||    | |   |    |  |||  | |    || |||   |||
CATTATTCCGAATTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATCGAACCACAGgtttg---aatcaagt---gctaaagtgactggatctatctaaatttttttatttattcttatcatgaaatgatttt-cag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 17
CATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAGgtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtctatttacaccattattgaacag---------
||||||||||| || |||||||| || ||||| || || ||||| ||||| ||||||||||||||||||  |  |   ||    ||| |    | |||||| | ||    ||      | ||  | |    | ||||  ||          
CATTACACAGAGTTGCCAGATATAAAACGTGTGATTGTAAATACACATGCAATTGAGCCACAGgtttgt-gtgatccattgc-ttttataatttatctattgtaacattatgctagtttttaaattcttagtcattgttcaattcttgcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 17
CATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAGgtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtctatttacaccattattgaacag---------
||||||||||| || |||||||| || ||||| || || ||||| ||||| ||||||||||||||||||  | ||   ||    ||| |    | |||||| | ||    ||      |  |  |||    | ||||  | |         
CATTACACAGAGTTGCCAGATATAAAACGTGTAATTGTAAATACACATGCAATTGAGCCACAGgtttgt-gtgttccattgc-ttttataatttatctattgtaacatcatgctagttttaaaatacttagtcattgttcggttcttgcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 18
CATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAGgtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtctatttacaccattattgaacag-----
||||| || || || || || ||||| |||||||| |||||||| |||||||||||||||||||||| | ||   || |  |    ||   |   |||||  | | |   |    |  |||   || |  |||||     |      
CATTATACTGAGTTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATTGAGCCACAGgttt-tgattccaactactcaaatgacaca-atctatcgtaaatttgttttatattcttactatatgattatgatgtatttcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 18
CATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAGgtttgt----tatcttaagtta----tgctttgttgcctgtctattattactggctggggtggtctatttacaccattattgaacag-------------
|||||||||||||||||||| ||||| ||||| || || ||| | ||||| ||||| || ||||||| |    | |  |   ||     |  |||  ||  |  | ||||  ||    || | ||  || || | |    || | |  |              
CATTACACAGAATTACCAGACATCAAACGTGTGATTGTTAATTCACATGCAATTGAACCTCAGgtttatgtgctgttctgcttttaatctattttagtgtttaacaattaaaacccattgtg-tgagcttttaaaatacctactcattatgtggttgttacag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 18
CATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAGgttt--gttat-----cttaagttatgctttgttgcctgtctat-tattactggctggggtggtctatttacaccattattgaacag-----
||||| || || || || || ||||| |||||||| |||||||| ||||||||||||||||||||||   ||       || || | |   | | ||   | | ||| |||   |   |   ||  |||    | |  |||||     |      
CATTATACTGAGTTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATTGAGCCACAGgttttgattgcaactgctcaaatgacaatctattatatatatatatatatatatatattgtattcttacaatatgattataatgtatttcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 18
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 18
CATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAGgtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtctat-ttacaccatt--attgaacag
|||||| |||| ||||| |||||||| ||||| || ||||| || ||||| |||||||||||||| |    ||| || | ||  || |||||    | | |     ||     | || |  || |  | | | |  | |   |||
CATTACTCAGAGTTACCTGATATCAAACGTGTAATTGTGAACACACATGCTATTGAGCCACAGgtattacctctgaactaattgttggttgctaaacaact--cgatgttcaagttgctgaatatccctctactcaaatttgcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 18
CATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAGgtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtctatttacaccattattgaacag-----
||||| || ||||| || |||||||| |||||||| ||||| || ||||||||||||||||||||| | |     ||||   | |   |  | |||    ||||  ||  ||  ||  | | ||   || || || | | |      
CATTATACTGAATTGCCCGATATCAAACGTGTCATTGTGAACACACATGCCATTGAGCCACAGgttagatgctcaaagt---gttacataacttgtt--ctatt--tgaatgtagtatttttttctaactat-atggtatatttcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 18
CATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAGgtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtctatttacaccattattgaacag
||||| || || || |||||||| || || ||||| |||||||| ||||| |||||||||||||||| |   ||| |  | || ||  | |            |  |      | |  |  ||         | || |    
CATTATACTGAGTTGCCAGATATAAAACGCGTCATTGTGAATACACATGCAATTGAGCCACAGgtttttatacttcaactgtgtttcttggttcactaggaggttgtaaacttgctattgaatacgtggttctcttcag---

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: 63 (upstream exon), 75 (downstream exon)
Score: 89

CATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAGgtttgttatc ... tattgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG




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