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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAGgtatccttttaattcatttcaatgcatagtcggtatgtaatacctttgcttttttaccatgaaattcagttgtgtcttgccttaccatgcccattttttaacag

Basic information

species Oryza sativa
transcript LOC_Os11g01380.1
intron # 15
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 15
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 13
GGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAGgtatccttttaatt-----catttcaatgcatagtcg-----gtatgtaatacctttgctttttt---accatgaaattcagttgtgtcttgccttaccatgcccattttttaacag-----------------------
|||||||||||||||||  | |||||||||||||||||||| || |||||||| || ||||| ||||| ||||||||||||||||||||||| |||  |||     ||| | ||| | |    |     |||| ||| |   ||  || | |   | |     || ||||| | |    | | || |||    ||  ||    |                       
GGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAGgtatcttttgtattattagcatataaattcttttctgtagtagtatataaaattctttgttgtctgggaactctccatgcagttcttttagtcttcactatgtaatttggttttttgctttggcttacattcttcaacag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 15
GGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAGgt-atccttttaattcatttca------atgcatagtcggtatgtaatacctttgcttttttaccatgaaattcagttgtgtcttgccttaccatgcccattttttaacag
|| ||||| || |||||  | |||||||| ||||||||||| || || |||||||||||||| || ||||||||||| || ||||||||  |   | || |    || |      ||| | | | |  || |||||    |||||  | | |||    || |  | ||   ||  |    |||               
GGTGCTGTTAATTTTGCATTAATGATGTCGCAAATGGAGGGAGGTTGCCCAGTTGATTACAACACCATAACTGATCTGTTTCTTCAGgttgtttgtctactgtgattaagccattatggagattagtaatataatattgctgcttcatcatcattttttttatgtatgaaatgtttctttatgtggc-----------

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 15
GGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAGgtatccttttaattcat--ttcaatgcatagtcggtatgtaatacctt-tgcttttttaccatgaaattcagttgtgtcttgccttaccatgcccattttttaacag
|||||||| || ||||| || |||||| | |||||||| || || || ||  |||| ||||| || |||||||||||||| |||||||| |  |   | || |   || | |   |    | ||| |  | | || | || || ||   |   ||||||||||        ||   | | |  | | ||     
GGAGCTGTAAATTTTGCTCTGATGATGGCTCAAATGGAAGGAGGATGCCCCATTGACTACAACACAATAACTGATCTCTTTCTTCAGgtttattcgcagtttaccctttagtatcttcatgatatttggttcattgttctcttataatttattattcagttgta----attttgaaaagacagtatcttgt---

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 15
GGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAGgtatccttttaattcatttcaatgcatagtcggtatgtaatacctttgc-ttttttaccatga-----aattcagttgtgtcttgcctt----accatgcccattttttaacag----------------
|| ||||| || |||||  | |||||||| ||||||||||| ||  | |||||||||||||| || |||||||||||||| |||||||| |  || ||  |  |    | |||     | |   || ||   |    ||||||  |||||      ||| |||  ||  | |   |    |  ||    |||||      |                
GGCGCTGTTAATTTTGCATTAATGATGTCTCAAATGGAGGGAGGTAGCCCAGTTGATTACAACACAATAACTGATCTCTTTCTTCAGgt-tgattatatgttgtgattaagcaattatgatgaatattaatatgatattttttttcatgatcattgatttagtactgaatggttcttgaaattattgttattttcattttggttactttctgctcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 15
GGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAGgtatccttttaattcatttcaatgcatagtcggtatgtaatacctttgcttttttaccatgaaattcagttgtgtcttgccttaccatgcccattttttaacag
|| ||||| || |||||  | |||||||| ||||||||||| || || |||||||||||||| || ||||||||||| || ||||||||    | |  | |    | ||  |||  |    || || ||   |    ||  | |      ||    || | | ||| | ||  |      | |||     |
GGTGCTGTTAATTTTGCATTAATGATGTCGCAAATGGAGGGAGGTTGCCCAGTTGATTACAACACCATAACTGATCTGTTTCTTCAGgttgtttatctactgtgattaagccattatgaagat-tagtaatataatattcctgcttcatgatc--attat-tgttgacatatgaaatgtttctttatgtgg

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA14G06340.2 (Glycine max), 5'ss of exon 15
GGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAGgt--atccttt--------taattcatttcaatgcatagtcggtatgtaatacctttgcttttttaccatgaaattcagttgtgtcttgcctt----accatgcccattttttaacag----------------
|| ||||| || |||||  | |||||||| ||||||||||| ||  | |||||||||||||| || |||||||||||||| ||||||||  ||  | |        |||   ||||  ||| ||| |    || | |||  |||| ||  | | |||  | || |||  ||  | |   |    |  ||    |||||  |   |                
GGCGCTGTTAATTTTGCATTAATGATGTCTCAAATGGAGGGAGGTAGCCCAGTTGATTACAACACAATAACTGATCTCTTTCTTCAGgttgattatatgttgtgattaagcaattttgatgaatatta---atatgatatttttgtttcataatcattga-tttagtactgaatggttcttgaaattattgttattttccatttggttacttcctgctcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 13
GGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAGgtatccttttaattcatttcaatgcatagtcggtatgtaatacctt-tgcttttttaccatgaaattcagttgtgtcttgccttaccatgcccattttttaacag--
|| ||||| || ||||| || |||||||| |||||||||||||| || || ||||| || || || ||||| |||||||| |||||||| |   |   |||  ||  | ||| |    | | |    | | || | || || || |||    ||   ||  |     || |   | |       | | |||   
GGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAGGGGGGTTGCCCTGTTGACTATAACACAATAACCGATCTCTTTCTTCAGgtttatct---atttcttctattgctttaatgatgttgggttcattgtcctcttctatcat----ttatatttcgatccaccatttaaagaatgaagtatcacatat

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 15
GGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAGgtatccttttaattcatttcaatgcatagtcggtatgtaatac-ctttgcttttttaccatgaaattcagttgtgtcttgccttaccatgcccattttttaacag
|| ||||| || ||||| || |||||||| |||||||||||||| || || ||||| ||||| || |||||||||||||| |||||||| |  | ||  |  |||  | ||| |    | | |    | |  |||||| |  || | | ||      ||  |     || |   | |       | | ||| 
GGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAGGGGGGTTGCCCTGTTGACTACAACACAATAACTGATCTCTTTCTTCAGgt-ttatcttgttctattctattgctttaatgatgttgggttcattttgctctcctatctttaat----atttcgatccaccatttaaagattgaagtatcacat

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 15
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 15
GGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAGgtatccttttaattcatttcaatgcatagtcggtatgtaatacctttgcttttttaccatgaaattcagttgtgtcttgccttaccatgcccattttttaacag
||||| || || |||||  | |||||||| |||||||| || || ||||||||||| ||||| ||||| |||||||| |||||||||||   |   ||    ||   | ||  ||      ||   ||  | || ||| |||  || || |   | |  |||  |    |||  | |   |   |   |||
GGAGCAGTAAATTTTGCTTTAATGATGTCCCAAATGGAAGGAGGTTGTCCAGTTGACTACAACACTATCACTGATCTTTTCCTTCAGgtgaacacgtagaatat---actgtgtacataaaattgtatctcattacttgtttcacaagagagcta-tcatgtgctaatgtact-tacttttgcatattcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 15
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 15
GGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAGgtatccttt-taattcatttcaatgcatagtcggtatgtaatacctttgcttttttaccatgaaattcagttgtgtcttgccttac-catgcccattttttaacag
|||||||| || |||||||| |||||||| ||||||||||| || |||||  ||||||  ||||| |||||||||||||| |||||||| |  | | | | |  |  |  |    | |   ||| ||||| | |    |   |    | | |||   | ||  |    |||     |  |||      |    
GGAGCTGTAAATTTTGCGCTAATGATGTCTCAAATGGAGGGAGGTTGTCCCATTGATTTTAATACGATAACTGATCTCTTTCTTCAGgtttgttatgtgactgctgcctctattaattgaatatataatatcataa--tcactgatcttacattttttggtaaccaatcttgtatctttccacaccgca----

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 15
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 15
GGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAGgt---atccttttaattcatttcaa--tgcatagtcggtatgtaata-cctttgcttttttaccatgaaattcagttgtgtcttgccttaccatgcccattttttaacag
|| || || || |||||  | |||||||| |||||||| || || || |||||||||||||| || ||||| ||||| |||||||||||   ||   | |  | | ||| |   ||   |||     |  || |  |     |||  | |  || ||  ||      |   | || |     |  |  ||| |    
GGGGCAGTTAATTTTGCTTTAATGATGTCTCAAATGGAAGGAGGTTGCCCAGTTGATTACAACACAATAACAGATCTATTCCTTCAGgttgaatgaatgttttcctttttatgttgtcaagtttaggtacaaaagtcaccaatttcatcctttggaaaaca------tacagtctaatggatctgaactttga----

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: 60 (upstream exon), 73 (downstream exon)
Score: 129

GGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAGgtatcctttt ... tttttaacagAGAAACATGATACGTGAGGCAACAGCTTTCCTGCTGGATGTTTTAAAGCCAAACTTGCCGGAGCATGCTTTTCTTCAAACCAAG




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