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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACCCAAAGGCCTTTTCCAGTGCAGATACAGCTTATGTCCTTGCTTATTCAGTCATAATGCTCAACACCGATGCACATAATCCAATGGTAAAAAATAAGgtatgtatcttattggctaagtttttgtgtaatataccatagacagcctttggttctgttgtgatgtattaattaatgcag

Basic information

species Oryza sativa
transcript LOC_Os03g14260.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14260.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G058870_T01 (Zea mays), 5'ss of exon 4
CAACCCAAAGGCCTTTTCCAGTGCAGATACAGCTTATGTCCTTGCTTATTCAGTCATAATGCTCAACACCGATGCACATAATCCAATGGTAAAAAATAAGgtatgtatcttattggctaagtttttgtgtaatataccatagacagcctttggttctgttgtgatgtattaattaatgcag
 || ||||||||||||||||||||||||||||||||||| || |||||||||||||||||||| ||||| ||||||||||| |||||||| ||||||||||||  | |||| | |   | ||| || ||     | |        |  ||      |  ||| |  | ||| |  ||||||
TAATCCAAAGGCCTTTTCCAGTGCAGATACAGCTTATGTTCTGGCTTATTCAGTCATAATGCTTAACACTGATGCACATAACCCAATGGTCAAAAATAAGgtactt-tcttgtggtgaaggttcttttgcggagttct-------ggtttacacaattatgtaacatgttactcgatgcag

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA03G02610.1 (Glycine max), 5'ss of exon 4
CAACCCAAAGGCCTTTTCCAGTGCAGATACAGCTTATGTCCTTGCTTATTCAGTCATAATGCTCAACACCGATGCACATAATCCAATGGTAAAAAATAAGgtatgt-----atcttattggc---taagtttttgtgtaa-----tataccatagacagcctttggttctgttgtgatgtattaattaatgcag
 || |||||||||||||| ||||| || ||||| ||||||||||| ||||| || ||||||||||| || ||||| || ||||| ||||| || |||||||| ||      ||| ||| |     ||| ||  |||  ||     |||  || | |       |  || | || |    | || | | ||||||
TAATCCAAAGGCCTTTTCTAGTGCTGACACAGCATATGTCCTTGCCTATTCTGTTATAATGCTCAATACAGATGCTCACAATCCTATGGTGAAGAATAAGgtgtgctcacaatcctatagttctgtaaattgatgtacaaataattatgtcagacatgatggcttattttctttttggttgttgagttatgcag

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA09G40480.1 (Glycine max), 5'ss of exon 4
CAACCCAAAGGCCTTTTCCAGTGCAGATACAGCTTATGTCCTTGCTTATTCAGTCATAATGCTCAACACCGATGCACATAATCCAATGGTAAAAAATAAGgtatgt-------atcttattggctaagtttttgtgtaata-----taccatagacagcctttggttctgttgtgatgtattaattaatgcag
 || ||||| | |||||| ||||| |||||||| ||||||||||| ||||| || ||  |||| || |||||||| || ||||| ||||| ||||| |||||  |        ||  ||   | | | ||||  | | ||      ||  ||| |     |  |||||  || |  |  ||| | | ||||||
TAATCCAAAAGTCTTTTCTAGTGCTGATACAGCATATGTCCTTGCATATTCTGTGATTCTGCTTAATACCGATGCTCACAATCCTATGGTGAAAAACAAGgtgcggtctgtcaattctagaagttga-ttttcatatgattgtgattatgatatatgtaatgaggttc--tttttgttcattgagttatgcag

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA18G45340.1 (Glycine max), 5'ss of exon 4
CAACCCAAAGGCCTTTTCCAGTGCAGATACAGCTTATGTCCTTGCTTATTCAGTCATAATGCTCAACACCGATGCACATAATCCAATGGTAAAAAATAAGgtatgt-----atcttattggc---taagtttttgtgta-atataccatagaca-gcctttggttctgttgtgatgtattaattaatgcag---------
 || |||||||||||||| ||||| || ||||| |||||||| || ||||| || |||||||| || || ||||| || ||||| ||||| || |||||||| ||      ||||||| |     ||| ||  |||  | ||||  | | || | |  |||||  ||  |  | |   ||  || ||             
TAATCCAAAGGCCTTTTCTAGTGCTGACACAGCATATGTCCTAGCCTATTCTGTTATAATGCTTAATACAGATGCTCACAATCCTATGGTGAAGAATAAGgtgtgctcacaatcttatagttctgtaaattgatgtacacatatggctttgatatgtttttggaccttgtaagttagtttttttcatttttagttcctgt

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA01G34560.1 (Glycine max), 5'ss of exon 5
CAACCCAAAGGCCTTTTCCAGTGCAGATACAGCTTATGTCCTTGCTTATTCAGTCATAATGCTCAACACCGATGCACATAATCCAATGGTAAAAAATAAGgtatgtatcttattggctaagtttttgtgt-aatataccatagacagcctttggttctgttgtgatgtattaa-ttaatgcag------------------
 || |||||||||||||| ||||| || || || |||||||| || ||||| || |||||||| || || ||||| || ||||| ||||| || |||||||| ||      ||    ||  | | |   |  || ||| | | |  || ||    | | ||| ||  |  ||| ||| ||                     
TAATCCAAAGGCCTTTTCTAGTGCTGACACTGCATATGTCCTAGCCTATTCTGTTATAATGCTTAATACAGATGCTCACAATCCTATGGTGAAGAATAAGgtgtgctcacaatcttatagttctgtaaattgatgtac-acataaggctttgatatgttttgggaccttgtaagttagtgttttttcatttttagtccctg

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA18G45360.1 (Glycine max), 5'ss of exon 3
CAACCCAAAGGCCTTTTCCAGTGCAGATACAGCTTATGTCCTTGCTTATTCAGTCATAATGCTCAACACCGATGCACATAATCCAATGGTAAAAAATAAGgta-----tgt--atcttattggctaagttt-------ttgtg-taata--taccatagacagcctttggttctgttgtgatgtattaattaatgcag
 || ||||| | |||||| ||||| |||||||| ||||||||||| ||||| || ||| |||| || |||||||| || ||||| ||||| ||||| |||||      |||  ||  ||   | | | |||       || || | ||   ||  ||| |     |  |||||| || || | |  | | | ||||||
TAATCCAAAAGTCTTTTCTAGTGCTGATACAGCATATGTCCTTGCATATTCTGTGATACTGCTTAATACCGATGCCCACAATCCTATGGTGAAAAACAAGgtgcagtctgtcaattctagaagttgattttcatatgattatgattatgattattatatatgtaatgaggttcttttttg-tttgctgagttatgcag

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 5'ss of exon 4
CAACCCAAAGGCCTTTTCCAGTGCAGATACAGCTTATGTCCTTGCTTATTCAGTCATAATGCTCAACACCGATGCACATAATCCAATGGTAAAAAATAAGgtatgtatctta-----ttggctaagt--ttttgtgtaatataccatagacagccttt------ggttctgttgtgatgtattaattaatgcag-----------------------------------------
|||||||||||  ||||| || || ||||| || |||||||| ||||| ||||||||  |||||||||| ||||||||||| || ||||| || |  ||||||  ||| | |     || ||| ||    ||| || |||    | |    |   | |      | |  ||||   |  |  | |||  |  |                                          
CAACCCAAAGGATTTTTCTAGCGCTGATACGGCATATGTCCTCGCTTACTCAGTCATTTTGCTCAACACAGATGCACATAACCCTATGGTGAAGAGCAAGgtacatatttgagctgtttcgcttagaagctttctgaaatccctcttgaggaatatcttaatacgatcttgtttgaagcttgtgattggtcaaacaaagtaactcattactaaatttttcaattacaacttgcag

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 5'ss of exon 4
CAACCCAAAGGCCTTTTCCAGTGCAGATACAGCTTATGTCCTTGCTTATTCAGTCATAATGCTCAACACCGATGCACATAATCCAATGGTAAAAAATAAGgtatgtatcttattggctaagttt----ttgtgtaatataccatag-acagcctttggttctgttgtgatgtattaattaatgcag------------------
 || |||||||| ||  | |||||||| ||||| ||||||||||||||||| || || ||||| || |||||||| ||||| || ||||| || ||||||||||    || |     | | |||    || ||  || |   |||  | | | |   |   |  |||    ||||||||  |                      
TAATCCAAAGGCTTTCACTAGTGCAGACACAGCCTATGTCCTTGCTTATTCTGTTATTATGCTGAATACCGATGCTCATAACCCGATGGTTAAGAATAAGgtata---ctcaaaaatttaatttgaagttatgagatgtttaatatcataacttgctgaatttctgtttattattaatttttttttggtcattaaaatatgcag

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S264_74V6.1 (Physcomitrella patens), 5'ss of exon 5
CAACCCAAAGGCCTTTTCCAGTGCAGATACAGCTTATGTCCTTGCTTATTCAGTCATAATGCTCAACACCGATGCACATAATCCAATGGTAAAAAATAAGgtatgtatcttattggctaagtttttgtgtaatataccatagacagcctttggttctgttgtgatg--tattaattaatgcag------------------
||| || ||||| ||   |||||||||||||||||| || |||||||| || || || |||||||| || ||||| || || || ||||| || |  |||||  ||    | ||| | |  |     ||   |  |   |  | |   ||    |  ||| || ||    |  | |  | |                    
CAATCCGAAGGCATTCAGCAGTGCAGATACAGCTTACGTTCTTGCTTACTCTGTGATCATGCTCAATACTGATGCTCACAACCCCATGGTCAAGACCAAGgtcagtgatctgttg-caatttcacactgcgttcaagtgtgcatatttttgctctgagttctgctgatcctagacttttacgatatactttggccttttcc

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S11_55V6.1 (Physcomitrella patens), 5'ss of exon 5
CAACCCAAAGGCCTTTTCCAGTGCAGATACAGCTTATGTCCTTGCTTATTCAGTCATAATGCTCAACACCGATGCACATAATCCAATGGTAAAAAATAAGgtatgtatcttattggctaagttt-ttgtgtaatataccatagacagcctttggttctgttgtgatgtattaattaatgcag-------------------
||| || ||||||||    |||||||||||||| || || |||||||| || || || ||||| ||||||||||| || || || ||||| |||| ||||||  |||   | || |    |    ||| || |  |||    |   |    ||  | | |||   ||   |   |  ||  |                   
CAATCCGAAGGCCTTCAGTAGTGCAGATACAGCATACGTGCTTGCTTACTCTGTGATCATGCTTAACACCGATGCCCACAACCCTATGGTCAAAACTAAGgtcagtaatatgttagaatcgcgcattgcgtga-gtacgggtgcgtgtgcgtgtgtgtattgctttgctcttggttctgttgctcttacattgttgcgtta

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: 67 (upstream exon), 75 (downstream exon)
Score: 42

CAACCCAAAGGCCTTTTCCAGTGCAGATACAGCTTATGTCCTTGCTTATTCAGTCATAATGCTCAACACCGATGCACATAATCCAATGGTAAAAAATAAGgtatgtatct ... attaatgcagATGTCACCAGAAGATTTCATTAGAAACAATCGAGGTATTGACGATGGGAAAGACCTGCCTGAAGAATTTATGAGGTCCTTATATGAAAGGATTTGGAAAA




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