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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttcacctaatgggcaactgatgagattcactactgtctcaaggctaaccagtggtttgttaactttcag

Basic information

species Zea mays
transcript GRMZM2G435582_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G435582_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttcacctaa-tgggcaactgatgagattcac----tactgt------ctcaaggctaaccagtggtttgttaactttcag
 ||||||||||| ||||| ||||| |||||||| || |||||||||||||||||||| ||||| ||||| || ||||||||||| ||||||||||| ||||||| ||  || | || |     | | ||||| |  ||    |||| |      ||||| |||||    || ||| |  ||||||||
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcag

upper sequence: GRMZM2G435582_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 21
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttcacctaatgggcaactgatgagattcactac------tgtctcaaggctaaccag----tggtttgttaactttcag
 || || |||||||| |||||||| |||||||| || || |||||||||||||| || || |||||||| || || |||||||| |||||||| || ||||||||| |      | |       |  || | |  | | |      ||  |||  |  ||  |     ||||||  |   || |||
TGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTTCAATGTCCAGCATTACTTCAAAGgtattaatgttgtaagttacttttttttgtggtgtatttccttgtatgcttcagtgacaagaaaaatatggttttgtttgttgcag

upper sequence: GRMZM2G435582_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA17G13850.1 (Glycine max), 5'ss of exon 20
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgta----ttatttcacctaatgggca-actgatgaga--ttcactactgtctcaaggctaaccagtggtttgttaactttcag---------
 || || ||||| ||||| ||||| |||||||| || ||| | || |||||||| || ||||| |||||||| || || ||||| || || |||||||||||     || | || |   | | | | | ||||   |  || | || | |  |   ||  || | |  |||  |  | |             
TGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTTCTATGTCAAGTATCACATCTAAGgttaaatttgtctctctctaagtgtatattgatttcacctttattagt-ttgctgtgcatacaactcattttcttgcctctttttgcttcag

upper sequence: GRMZM2G435582_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 18
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattattt-cacctaatgggcaactgatgagattcactactgtc---tcaag-gctaaccagtggtttgttaactttcag------
 || || |||||||| |||||||| |||||||| || || || ||||||||||| || || ||||| || || || |||||||| ||||||||||| ||||||||| || ||  |          |      | ||  || | ||   |||     |||      |  | ||   |||  |      
TGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTTCAATGTCCAGCATTACATCCAAGgtattagttgcaaatttaaactgttttgctctactctgtattttcctttcattcattaagtgacaggatattgtttttttgttgcag

upper sequence: GRMZM2G435582_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G17410.1 (Glycine max), 5'ss of exon 17
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatt----tcacctaatgggcaactgatgagattcactac-tgtctca-----aggctaaccagtggtttgttaactttcag
 || || |||||||| |||||||| |||||||| || || |||||||||||||| || || |||||||| || || |||||||| |||||||| || ||||||| | |    | |  || |       |  ||   |||  |   ||  |||     | |  || ||  | ||||||   || |||
TGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTTCAATGTCCAGCATTACTTCAAAGgtatcaatattgtaaattactttttttgttgtgtatttccttgtatgcttcagttacaagaaaaacatggttttgtttg-ttgcag

upper sequence: GRMZM2G435582_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA10G02410.1 (Glycine max), 5'ss of exon 18
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttc---acctaatgggcaa----ctgatgagattcactactgtctcaaggctaaccagtggtttgttaactttcag------
 || ||||||||||| |||||||| |||||||| || || |||||||||||||| || || ||||| || || || |||||||| |||||||| || ||||||||| ||    |  |||   |       ||  |  |  |  |   |   |||    | ||  |     | ||   |||  |      
TGGCCCTCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTTATTAACATTTCAATGTCCAGCATTACGTCCAAGgtattagttgcaaatttaaacagttttgctctactttgtatttcctttcattcataagtgacaggatagatattgtttttttgttgcag

upper sequence: GRMZM2G435582_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 21
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttcacctaatgggcaactgatgagattcactactgtctcaaggctaac-cagtggtttgttaactttcag----------
 ||||||||||| |||||||| || ||||| || ||||||||||||||||| || ||||| |||||||||||||| |||||||| |||||||| || ||||||   | |||   | ||   |  ||||    ||   | || |||       |    | | |    || ||  | |           
TGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCTCAATGTCCAGCATTACTTCGAAGgtaac-tctcataaagtg---atatgatttccttttatgctttcttttaatgattgtacttgaccatttacactaaatgctttgcag

upper sequence: GRMZM2G435582_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttcacctaatgggcaactgatgagattcac-tactgtctcaaggct---aaccagtggt-ttgttaacttt-cag
 ||||||||||| |||||||| || |||||||| |||||||| ||||  ||||| |  || || |||||||| || |||||||| ||||| ||||||||||||       ||   |||   |  |     |||| ||  || |  ||     |   |||  ||| | || ||||   | |||
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactgaatactctatgaaaagttctaccgatttacacacgggatctttttttcaaacttgtgttcttcttaatactgcag

upper sequence: GRMZM2G435582_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttcacctaatgggcaactgatgagattcactactgtctcaaggctaaccagtggtttgttaactttcag--------------------------
 || || ||||| || || || || |||||||| || || || || |||||||| || || || ||||||||||| |||||||| ||||| |||||||||||  |  || |   | | |     |  |   || |  |  | ||| |  |        |  ||| ||   | ||||                          
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgata-agtagcttcttttttctatcccttgatctct-atagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag

upper sequence: GRMZM2G435582_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 21
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtat-tattt-cacctaatgggcaactgatgagattc--------actactgtctcaaggctaaccagtggtttgtta--actttcag
 || |||||||| ||||||||||| |||||||| || || || |||||||| ||||| || ||||| ||||| ||||||||||| || || || || ||||||  ||| | || | ||  ||  |||    || |          | |  ||| |  |   ||          || ||   ||| |||
TGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATATCAATGTCTAGTATCACTTCAAAGgtaaatatgtgcatcaaaatggtgactatgcagctctcttttgcaagtcttgttttgaaaatatttgacatcctgatattgcttgcag

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: 49 (upstream exon), 31 (downstream exon)
Score: 80

CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttc ... taactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGTTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 68

CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttc ... taactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGTTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 118

CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttc ... taactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGTTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG


Block sizes: 49 (upstream exon), 32 (downstream exon)
Score: 39

CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttc ... taactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGTTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG