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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAGgtatttccttttatctctgttagacctctattgttttgtcaatgttgttgtgcctcttaatttttgttcctgttctctag

Basic information

species Zea mays
transcript GRMZM2G426306_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G426306_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g02850.2 (Oryza sativa), 5'ss of exon 4
ATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAGgtatttccttttatctctgttagacctc--tattgttttgtcaatgttgttgtgcctcttaatttttgttcctgttctctag
 || | |||||||||||  | ||| | || ||||||||||||||||| || ||||| || |||||||||||||||||||||||||| ||||||||   |  ||||| ||  | || |  |   | ||||    |   |||| |||| |   ||  ||  || |    ||   |||
GTATTTCAACATGTGCTCATTGATTTTCCGGGGCTTGCATTCTTCACAACCTATGCTCTGTTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgt---tagtttta-cttggatatattttggttttgtcccatgggtgtttttgttctcattggttcatgatggcatttgttag

upper sequence: GRMZM2G426306_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G06700.1 (Glycine max), 5'ss of exon 5
ATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAGgtatttccttttatctctgttagacctctattgttttgtcaatgttgttgtgcctctta-atttttgttcctgttctctag-------------------------------------------------------------
                                 ||||| ||||| || |||||||||||||| || || |||| ||||||||||||||| |||| |     ||| || | || |  |      ||| ||   ||  |||| | |||||| ||   |||| ||| |       ||                                                             
--------------------------------TCTTGCTTTCTTTACAACATATGCACTTTTGgtcctgttctaggctgagatttattaccaggcaag---tttgatttgtggtgcat-----ttgcttctacatggttggtttgcctcctatgattttcttcttccatggcagtgtgttttgctgattggttttgatgggctaattaccacctgggtgttaaatgcttttgcag

upper sequence: GRMZM2G426306_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G28990.1 (Glycine max), 5'ss of exon 4
ATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAGgta--tttccttt----tatctctgttagacctctattgttttgtcaatgttgttgtgcctctt--aatttttgt-tcctgttctctag--------------------------------------------
||  | |||||  |  | || ||  ||||  | ||||| ||||| || |||||||||||||| || || ||||||||||||||||||||||||| |  |||  |||    |   | || |    |    ||| |||| |     || | | | ||||  |  |  ||| |  || |   | |                                            
ATTGTTCAACACATCTTGCTTGACGTGCCGAGTCTTGCTTTCTTTACAACATATGCACTTTTGGTCCTGTTCTGGGCTGAGATTTATTATCAGgcaagtttgatttgtggtgcatttgcttctacatggttggtttgcctcctgtgattttcttcttccaggtagtgtgttttgctgattggttttgatgggctgattactgcctcggtgttaaatgctttttcag

upper sequence: GRMZM2G426306_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA20G01360.1 (Glycine max), 5'ss of exon 4
ATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAGgtat-ttccttttatctctgttagacctctat-tgttttgtcaatgttgt-tgtgcctcttaatttttgttcctgttctctag---------------------------------------------------
||  | |||||  |  | || ||  ||||  | ||||| ||||| || |||||||||||||| || || |||||||||||||||||||| |||| |  ||   ||| |      |   | ||||  || || ||     |  | ||    ||||| |   ||    |||  | |                                                     
ATTGTTCAACACATCTTGCTTGACGTGCCGAGTCTTGCTTTCTTTACAACATATGCACTTTTGGTCCTGTTCTGGGCTGAGATTTATTACCAGgcaagtttgatttgtggtgcatttgcttctacatggttggtttgcctcctgtgattttcttattccatggcagtgtgttttgctgattggttttgatgggctgattactgcctcggtgttaaatgcttttgcag

upper sequence: GRMZM2G426306_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA05G26630.2 (Glycine max), 5'ss of exon 4
ATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAGgta-----------------------------tttccttttatctctgttagacctctattgttttgtcaatgttgttgtgcctcttaatttttgtt-cctgttctctag
||  | |||||| |  | || || |||||  | ||||| ||||| || || |||||||| || || || |||||||||||||||||||| |||| |                             |||| |||||  |   || |     |  | |||||      |  || || || | |   |  ||| ||||||    ||
ATTGTCCAACATATCTTACTTGACATGCCTAGTCTTGCTTTCTTTACAACTTATGCACTGTTGGTACTGTTCTGGGCTGAGATTTATTACCAGgcaagttgaattcgtggtgcatttttactgtttttctttttaattagcttgggatgttgctattttggtggcctgattatgactttgatgctacgttacctgtttggcag

upper sequence: GRMZM2G426306_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA02G19410.1 (Glycine max), 5'ss of exon 4
ATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAGgtatttccttttatctctgttagacctctattgttttgtcaatgttgttgtgcctctta-atttttgttcctgttctctag-------------------------------------------------------------
||  | |||||  |  | || || ||| |  | ||||| ||||| || |||||||||||||| || || |||| ||||||||||||||| ||||    |  ||| || | || |  |      ||| ||   ||  |||| | |||||| ||   |||| ||| |       ||                                                             
ATTGTTCAACACATCTTGCTTGACATGTCGAGTCTTGCTTTCTTTACAACATATGCACTTTTGgtcctgttctaggctgagatttattaccaggc---tagtttgatttgtggtgcat-----ttgcttctacatggttggtttgcctcctatgatttttttcttccatggcagtgtgttttgctgattggttttgatgggctaattaccacctcggtgttaaatgcttttgcag

upper sequence: GRMZM2G426306_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 4
ATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAGgtatttccttttatctctgttagacctctattgttttgtcaatgttgttgtgcctctta-atttttgttcctgttctctag---------
||  | |||||| |  | || ||||| ||  | ||||| |||||||| || ||||| ||| | || || ||||||||||| ||||||||||||||| || ||  |   | |  ||    | | || ||||||||||| |  | ||  | | | |||||  ||     ||| | |         
ATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAGgtagtttctaatgagtat-ctatgggtttctttttttgtcaatgcttctttggttttgatattttacttaacactcttttgattggacag

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: 49 (upstream exon), 9 (downstream exon)
Score: 8

ATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAGgtatttcctt ... tgttctctagGCACGTGCCATGTCGACTGATGGGCTTAGACCAACTTTCTATTGGATCAACGGTGTGGTCTATGCAATTCAG




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