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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGTTTGAGAAGAACTTTGCTGTTAAGTTCCCAGCTTGCTCAATTGCTGCCAAGTGCCACATTGATCAAAGCACAACAATTCTTGATGTGCAAGGGGTGgtatgtatgtgcaaatatttggataattcattaaatgattgcacttttactatttataatctaagaaaaaaaatacatttttag

Basic information

species Oryza sativa
transcript LOC_Os02g24430.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g24430.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G162461_T01 (Zea mays), 5'ss of exon 5
GGAGTTTGAGAAGAACTTTGCTGTTAAGTTCCCAGCTTGCTCAATTGCTGCCAAGTGCCACATTGATCAAAGCACAACAATTCTTGATGTGCAAGGGGTGgtatgtatgtgcaaatatttggataattcattaaatgattgcacttttactatttataatctaagaaaaaaaatacatttttag
|||||| |||||||||||||||||||||||||||||||||||||| || || |||  ||| ||||| || ||||||||||||||||| |||||||| |||||| |||| | |||||   | | |   | | | |||| | ||  ||||||  |  |||| |       ||| | ||||||| ||
GGAGTTCGAGAAGAACTTTGCTGTTAAGTTCCCAGCTTGCTCAATCGCCGCGAAGCACCATATTGACCAGAGCACAACAATTCTTGACGTGCAAGGAGTGgtaggtatctacaaat---ttggtggct-actcaatggt-gcgattttacagtgaataacc-------aaagacacattttcag

upper sequence: LOC_Os02g24430.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA06G01270.1 (Glycine max), 5'ss of exon 4
GGAGTTTGAGAAGAACTTTGCTGTTAAGTTCCCAGCTTGCTCAATTGCTGCCAAGTGCCACATTGATCAAAGCACAACAATTCTTGATGTGCAAGGGGTGgtatgtatgtgcaaatatttggataattcattaaatgattgcacttttactatttataatctaagaaaaaaaatacatttttag------------------
 |||||||| | || ||| ||||||||||| || || || || || || || |||   |||||||| ||||||||||| ||| | ||||| ||||| ||||||||||        ||     | | |||| |     | |   | | | | |   | || | ||      |||||  ||   ||                  
AGAGTTTGAAAGGACCTTCGCTGTTAAGTTGCCTGCATGTTCTATCGCGGCAAAGAAGCACATTGACCAAAGCACAACTATTTTGGATGTTCAAGGAGTGgtatgtacaaaattctacagctacatttcagttctccaatc--cctctgccaaagaaaaaccaattgttgaaatattttaaaagtaatctccaatccctcta

upper sequence: LOC_Os02g24430.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA11G07660.1 (Glycine max), 5'ss of exon 3
GGAGTTTGAGAAGAACTTTGCTGTTAAGTTCCCAGCTTGCTCAATTGCTGCCAAGTGCCACATTGATCAAAGCACAACAATTCTTGATGTGCAAGGGGTGgta---------------tgtatgtgcaaatatttgg---ataattcat-taaatgattgcactttt-actatttataatctaagaaaaaaaatacatttttag
||||||||||| ||  |||| |||||||||  ||||||| ||||||||||| |||   ||||| |||||||| ||||| || || || ||||| || ||||||               | ||||||| || |        |||||| ||  |||| |||| || ||| |  ||   | | || | ||  | || |  |      
GGAGTTTGAGAGGACATTTGATGTTAAGTTTGCAGCTTGTTCAATTGCTGCAAAGAAGCACATAGATCAAAGTACAACTATCCTGGACGTGCAGGGAGTGgtaagaaaaatagttaattatatgtgccaagaacgaagtcataatttatacaaataattgtacatttgaacatggcttagcttaaaatgacaaaatgtac----

upper sequence: LOC_Os02g24430.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA11G12270.1 (Glycine max), 5'ss of exon 3
GGAGTTTGAGAAGAACTTTGCTGTTAAGTTCCCAGCTTGCTCAATTGCTGCCAAGTGCCACATTGATCAAAGCACAACAATTCTTGATGTGCAAGGGGTGgtatgtatg------tgcaa--atatt--tggataattcat---taaatgattgcactt-ttactatttataatc--taagaaaaaaaatacatttttag
 |||||||||||||  || | |||||||||||| || || |||||  | || |||   |||||||| ||||||||||| ||  | ||||||||||| ||||||||||||      |||||   || |  |  ||| ||  |   |   | |   | ||| || | |  |  || |   ||||  |||| |||  || || 
AGAGTTTGAGAAGACATTCGTTGTTAAGTTCCCTGCCTGTTCAATCTCAGCAAAGAAGCACATTGACCAAAGCACAACTATCTTGGATGTGCAAGGAGTGgtatgtatgaaattatgcaacagtactactaaatagtttttacttttctaacccctcttcttcccaaatcaaaccagcaagagtaaaagtactattataa

upper sequence: LOC_Os02g24430.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G05980.1 (Glycine max), 5'ss of exon 3
GGAGTTTGAGAAGAACTTTGCTGTTAAGTTCCCAGCTTGCTCAATTGCTGCCAAGTGCCACATTGATCAAAGCACAACAATTCTTGATGTGCAAGGGGTGgtatgtatgtgcaaatatttggataattcattaaatgattgcacttttactatttataatctaagaaaaaaaat-acatttttag------------------
|||||| |||| ||  || | ||| || ||  | |||||||| ||| |||| |||   ||||| |||||||| ||||| || |||||||||||||| |||||| ||||    ||||| || | | ||   ||||   |   || | ||    || | ||   || ||| || ||    || ||                    
GGAGTTCGAGAGGACATTCGATGTGAAATTTGCGGCTTGCTCCATTTCTGCAAAGAAACACATCGATCAAAGTACAACCATCCTTGATGTGCAAGGAGTGgtacgtat-cagaaatagtttgtttatc--ttaagccaacccaatattgaagttaaaaaataaaaaaacaacattgtgttcttgcaccaaagatcttaccatt

upper sequence: LOC_Os02g24430.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA16G24670.1 (Glycine max), 5'ss of exon 3
GGAGTTTGAGAAGAACTTTGCTGTTAAGTTCCCAGCTTGCTCAATTGCTGCCAAGTGCCACATTGATCAAAGCACAACAATTCTTGATGTGCAAGGGGTGgtatgtatgtgcaaatatttggataat--tcattaaatgattgcacttttactatttataatctaagaaaaaaaatacatttttag------------------------------------------------------------------------------------------------------
|||||| |||| ||  |||| ||| || ||| | |||||| | |||||||| |||   ||||| |||||||||||||| || |||||||||||||| |||||| |||   | ||   |||   || |   ||||  |  |||| | ||  |  |     |    ||    ||      || ||||                                                                                                       
GGAGTTCGAGAGGACATTTGATGTGAAATTCGCGGCTTGCACCATTGCTGCAAAGAAACACATCGATCAAAGCACAACCATCCTTGATGTGCAAGGAGTGgtacgtaacagaaatagtttatctattagccattccaatattgaagttaaaaaaccagcatgacaaattgaacttactatctttattcagttcacacttcaaaatgaaccttgatatctatgagaatgaaaaagaaatgtgtaaaatatgaaaaatatgatgaaaacttgctatgttttatctcacag

upper sequence: LOC_Os02g24430.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT2G18180.1 (Arabidopsis thaliana), 5'ss of exon 4
GGAGTTTGAGAAGAACTTTGCTGTTAAGTTCCCAGCTTGCTCAATTGCTGCCAAGTGCCACATTGATCAAAGCACAACAATTCTTGATGTGCAAGGGGTGgtatgtatgtgcaaatatttggataattcattaaatgattgcacttttactatttataatctaagaaaaaaaatacatttttag--
||||||||||| ||  ||   ||||||||||||||| ||||| || || || |||   |||||||||||||| ||||||||||||||||| ||||| |||||| |||       |||  || ||  | ||||    ||    |   |  | | | || | | || |      ||| ||  | |   
GGAGTTTGAGAGGACTTTCAATGTTAAGTTCCCAGCATGCTCCATCGCGGCAAAGAAGCACATTGATCAAAGTACAACAATTCTTGATGTCCAAGGAGTGgtacgtac------ataactgaatggt-catttgtagaaactataatagccaataatgaccaaaaatggtgtatatatgataaaag

upper sequence: LOC_Os02g24430.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT4G34580.1 (Arabidopsis thaliana), 5'ss of exon 4
GGAGTTTGAGAAGAACTTTGCTGTTAAGTTCCCAGCTTGCTCAATTGCTGCCAAGTGCCACATTGATCAAAGCACAACAATTCTTGATGTGCAAGGGGTGgtatgtatgtgcaaatatttggataattcattaaatgattgcacttttactatttataa-tctaagaaaaaaaatacatttttag-------
 ||||| |||||||  ||    || ||||||||  |||| ||  | || || ||    ||||||||||| ||||||||||||||||| |||||||| |||||| |||| |   ||||  |  ||   |   | |    || || ||  |   |   ||| |  || |       |   || | ||       
AGAGTTCGAGAAGACTTTCAAGGTCAAGTTCCCTTCTTGTTCTGTAGCAGCAAATAAACACATTGATCAGAGCACAACAATTCTTGACGTGCAAGGCGTGgtacgtattt---aataaattcatttctttatgatctctttcagttcaaaagtgggtaaattcaaaactgtgcgtgttttctgagtgattag

upper sequence: LOC_Os02g24430.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT4G36490.1 (Arabidopsis thaliana), 5'ss of exon 3
GGAGTTTGAGAAGAACTTTGCTGTTAAGTTCCCAGCTTGCTCAATTGCTGCCAAGTGCCACATTGATCAAAGCACAACAATTCTTGATGTGCAAGGGGTGgtatgtatgtgcaaatatttg-gataattcattaaatgattgcacttttactatttataatctaagaaaaaaaatacatttttag---------
||||||||||| || |||   ||||||||||||||| ||||| || || || |||   ||||||||||| |||||||| ||||||||||| ||||| ||||||||||     |||  | || || ||  | || ||||      ||||| |  | | | |   || |            |||| |         
GGAGTTTGAGAGGACCTTCAATGTTAAGTTCCCAGCGTGCTCTATCGCCGCGAAGAAGCACATTGATCAGAGCACAACTATTCTTGATGTCCAAGGAGTGgtatgtaaa---aaacctatgtgagaagaccttcaatg------cttttccagtatgtgactaaacatgcctttccttgtttttgttataacag

upper sequence: LOC_Os02g24430.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv03s0038g04480.t01 (Vitis vinifera), 5'ss of exon 4
GGAGTTTGAGAAGAACTTTGCTGTTAAGTTCCCAGCTTGCTCAATTGCTGCCAAGTGCCACATTGATCAAAGCACAACAATTCTTGATGTGCAAGGGGTGgtatgt----atgtg--caaatatttggataattcattaaatgattgcacttttactatttataatctaagaaa----aaaaatacatttttag--------------------------------------------------------------
||| ||||||| || |||    || |||||||||||||||||||| || || ||  | ||||||||||||||||| || ||||| ||||||||||| |||||| ||    || ||    || |     |  | | |   |   ||  ||||   |  |  | |   ||   ||     | || |  || |||                                                                
GGAATTTGAGAGGACCTTCAAAGTCAAGTTCCCAGCTTGCTCAATAGCAGCGAAAAGACACATTGATCAAAGCACCACTATTCTGGATGTGCAAGGAGTGgtacgttcgaatttggctcaagagaaaaactacttacatatcaatatcactgagaaaagatttttcctggaaagtcttagaagtggatgttttatttttgttgagctttgcttgtgaaaagatttcagtaagttaatattcaaaaatttgcctcag

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), 73 (downstream exon)
Score: 25

GGAGTTTGAGAAGAACTTTGCTGTTAAGTTCCCAGCTTGCTCAATTGCTGCCAAGTGCCACATTGATCAAAGCACAACAATTCTTGATGTGCAAGGGGTGgtatgtatgt ... acatttttagGGGATGAAACAATTCAGCAAAGCTGCAAGAGACCTCATTGGTCAGCTTCAAAAGATTGATGGTGATAACTACCCTGAG




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