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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgattatcagtttgttccaaaatatatattgactttttttttctaatttatctctgcttttagacccattttctattttgtggaagacaggttat...

Basic information

species Zea mays
transcript GRMZM2G000645_T02
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgattatcagtttgttccaaaatatatattgactttttttttctaatttatctctgcttttagacccatt--ttctattttgtggaagacaggttat-
||||||| |||||||||||||||||||| |||||||||||||||||| | || | ||||||  | |||||| |||||||||| |||||||||||||||| ||| ||   |  |  |||| ||||||| |   | |  ||||| ||||   |  | | |||   |||  |||  ||  ||   |||  |   |     |||   
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgact-tttgatccaaaacaatgagtttcttttattttggtacctgtttct--ctttgaacctgttgatttggtttcttaataattttgttcct

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os06g05180.4 (Oryza sativa), 5'ss of exon 1
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgattatcagtttgttccaaaatatatattgactttttttttctaatttatctctgcttttagacccatt--ttctattttgtggaagacaggttat-
                      |||||| |||||||||||||||||| | || | ||||||  | |||||| |||||||||| |||||||||||||||| ||| ||   |  |  |||| ||||||| |   | |  ||||| ||||   |  | | |||   |||  |||  ||  ||   |||  |   |     |||   
----------------------CAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgact-tttgatccaaaacaatgagtttcttttattttggtacctgtttct--ctttgaacctgttgatttggtttcttaataattttgttcct

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 17
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgattatcagtttgttccaaaatatatattgactttttttttctaatt-----tatctctgcttt-tagacccattttctattttgtggaagacaggttat
| ||| | || ||||||||||||||||| |||||||||||||| ||||||||    || ||  ||||| || |||| || || || | |||  |||| |||  |  || |   |  ||||| ||| | |   ||||| ||| |||   ||  |     |||   || | | |  |   |||    || || | |   ||||  |  
TGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCCAAAGAGCATCATAACAGg--taggact--taccttgttgcaagacaatgattgattttctttcaatatgtagaaatatgcttgatatgtgtagaaattaaaaatgtttttggtaacagaat--

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 17
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgt--ttgtgattatcagtt----tgttccaaaatatatattgactttttt-tttctaatttatctctgct---tttagacccattttctattttgtggaagacaggttat
||||| | ||||||||||| |||||||| ||||| |||||||| ||||||||    || ||  ||||| || |||| || ||||| | |||  |||| ||||  | || ||| || |||    |||| |  |||     ||   || ||| |||  || |||| | || |   ||| ||   |   | | || |  ||            
TACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCTAAAGAGCATCATAACAGgtagtagttattttctgttatgttgttacggaatgacccttactttctttatttagaaattatgtttgatatgttttgagaaaggcttttttgtaagggt----------

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 17
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgattatcagtttgttccaaaatatatattgactttttttttctaatttatctctgcttttagacccattttctattttgtggaagacaggttat
| ||| | || ||||||||||||||||| |||||||||||||| ||||||||    || ||  | ||| |  |||| || || || | |||  |||| ||||    | |  | |  ||||   |   |  |   | |   ||  |||    |  || | |     ||  |    | | | |       || |  | || |
TGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCCAAAGAGCATCATAACAGgtagaagttagttaccttgtgttacgttgcaagataatgattaattttctttcaatatgttgaaatatgcttgatatgtgtagaaattaaaaatgctttt

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 17
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 17
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttg-tgattatcagtttgttccaaaatatatattgactttttttttctaatttatctctgcttttagacccattttctattttgtggaagacaggttat-
|  | || ||  |||||||||||||||| ||||||||||| || ||||| ||  | || |   |||| ||| |  | || ||||| |  ||  |||| |||| || |   | | |  || |         | |  |  | || ||| ||  | || ||| || | |  ||    | ||   ||||           |  |  
TGTTGCTAAGCCTGATTGAGTACAAGACTCTTGTGATGCGGGGTGATTTAGACAAAGCCAGTGAAATCTTACCTACAATTCCTAAAGATCAGCATAACAGgtatgctagatcttaacttctgtgtgtgcttgtgatt-cattctttatcgcacttctct-tgttatgtgatatgtcttaggtttttcatttctttaggaagg

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 17
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgattatcagtttgttc-caaaatatatat---tgactttt--tttttctaa---tttatctctgcttttagacccatttt--ctattttgtggaagacaggttat----------------------------------------------
||||| | |||||||||||||||||||| |||||||||||||| |||||||| || || ||  || | ||| | || || ||||||| |||  ||||||||| || || | |   ||   || ||  ||   ||    ||  || |  | ||  |||   | ||||   | |   | |    |||    | ||||    ||  || |   |                                              
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 17
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 17
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgatta-tcagtttgttccaaaatatat--attgactttttttttctaatttatctctgcttttagacccattttctattttgtggaagacaggttat
| || || ||  ||||||| |||||||| ||||||||||| || |||||||||   || ||  |||||||| |  | || ||||| | |||  |||| | || ||| ||   | | |||| || ||| | | |  ||| |||| |  ||  |  ||||   |||| |||   | | | ||   |  | ||    |    |   
TGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCTAAAGAGCAGCATAACAAgtatgttataggttattttggtctaaattttttgcattcacttataattcattctttactactgcattttatctcttgttgcctgctatgtcctatgaat---

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 17
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 17
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgt-ttgtgattatcagtttgttccaaaatatatattgactttttttttctaatttatctctgcttttagacccattttctattttgtggaagac-aggttat
||||||| | |||||||||||||||||| ||||| |||||||| || ||  | | |||||   |||||||| | |  || ||| | | ||| || |||||||  ||  |||   ||| |  |   |   |  || |    |   |||  |  | ||  | ||   | ||       |   ||||  | |    | || ||  
TACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCTCAAGAGCACTACAATAGgtactgaaattcatagtatactgacagcaaagtaattgtgtgaatttgatggtgtagatgtgtcctcaggttgtagtctgatttgatagcttgctagatt--

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 17
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgattatcagt--ttgttccaaaatatatattgactttttttttctaatttat--ctctgcttttagacccattttctattttgtggaagacaggttat
||||||| |||||||||||||||||||| |||||||||||||| ||  |||| |  || ||  || ||||| | || || || || |  ||  |||||||||   |   ||    |   ||||   ||| |    |  | |           | |||       |  ||| || |   ||  | ||||||||   |     || 
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctactgttggctgttggtaaacaacagtaaaataagaggcaaacacttacaatgtagtatttggatc---ttcatgttttgtggggaattttgta-

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 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 192

TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgatt ... catatggcagTGTTGCTCATTTTTTGGAATCGAGAGGTATGTTGGAAGAGGCTCTTGAGATAGCCACTGATGCTGACTACAAGTTTGACCTAGCTGTGCAGCTTGGAAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 80

TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgatt ... catatggcagTGTTGCTCATTTTTTGGAATCGAGAGGTATGTTGGAAGAGGCTCTTGAGATAGCCACTGATGCTGACTACAAGTTTGACCTAGCTGTGCAGCTTGGAAAA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 72

TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgatt ... catatggcagTGTTGCTCATTTTTTGGAATCGAGAGGTATGTTGGAAGAGGCTCTTGAGATAGCCACTGATGCTGACTACAAGTTTGACCTAGCTGTGCAGCTTGGAAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 146

TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgatt ... catatggcagTGTTGCTCATTTTTTGGAATCGAGAGGTATGTTGGAAGAGGCTCTTGAGATAGCCACTGATGCTGACTACAAGTTTGACCTAGCTGTGCAGCTTGGAAAA