Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtatcatttatcctgcattgctctctacgtgtccatcaatatgtcaactaaactactacgtatttctacag

Basic information

species Zea mays
transcript GRMZM2G059893_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059893_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g42950.2 (Oryza sativa), 5'ss of exon 13
---------------------------------------CACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtatcatttatcctgcattgctctctacgtgtccatcaatatgtcaactaaactactacgtatttctacag----
                                       ||||||||||||||||||| |||||||| ||||| || |||||||||||||| || |||||||| | ||| |||  |    ||  | | | ||  ||||||||| |||||||| || | | || ||||||||    
CGGAGTACGTGATTCCTCTCGTCTTCCCACTGCTCACAGCACATCAACTGAATGTACAGCAATTTGCTAAGTACATACTATTTGTCAAGGATATCACAAGgtaccttttgtcccaccacacttgcgatgcgttaatcaatatgccaactaaattagtgcctacttctacagcaag

upper sequence: GRMZM2G059893_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g42950.1 (Oryza sativa), 5'ss of exon 13
---------------------------------------CACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtatcatttatcctgcattgctctctacgtgtccatcaatatgtcaactaaactactacgtatttctacag
                                       ||||||||||||||||||| |||||||| ||||| || |||||||||||||| || |||||||| | ||| |||  |    ||  | | | ||  ||||||||| |||||||| || | | || ||||||||
CGGAGTACGTGATTCCTCTCGTCTTCCCACTGCTCACAGCACATCAACTGAATGTACAGCAATTTGCTAAGTACATACTATTTGTCAAGGATATCACAAGgtaccttttgtcccaccacacttgcgatgcgttaatcaatatgccaactaaattagtgcctacttctacag

upper sequence: GRMZM2G059893_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA12G37070.1 (Glycine max), 5'ss of exon 13
---------------------------------------CACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtatcatttatcctgc--------attgc-tctctacgtgtccatcaatatgtcaactaaactactacgtatttct-acag------------------------------------------
                                       | || ||| ||||||| ||||| |||||||| |||||||| ||||||||||| ||      |||  ||||    |          |||    | ||   | |      || ||||  |   | |       || ||| |||                                           
CTGAGCATGTTCTTCCATTGCTTATACCCCTGCTGACTGCTCAACAATTGAATGTTCAACAGTTTGCCAAATATATGCTCTTTGTCAAGGATATGCTCCAgtaatattttcttttttaaaaaaaattaagcccctctattttttgttatctgtcttcctcattgtccttaatctctgacaaacttctctttaattttttttttgaactttgtgctctgtacag

upper sequence: GRMZM2G059893_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA09G00470.1 (Glycine max), 5'ss of exon 13
---------------------------------------CACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtatcatttatcctgcattgctctctacgtgtccatcaatatgtcaactaaactactacgtatttctacag----------------------------------------------------------------
                                       | |  ||| ||||||| ||||| |||||||| |||||||| ||||||||||| ||      |||   ||| |  |  ||   |||  ||    || ||| | | |  | | |  | ||   | | ||                                                                     
CTGAGCATCTTCTTCCATTGCTTATGCCCCTGCTGACTGCTCCACAATTGAATGTTCAACAGTTTGCCAAATATATGCTCTTTGTCAAGGATATGCTCCAgtaattttt-ttttaaataattcttaac---cccctcattttttttatttattttctgtctttctcattgtccttgatctctgacaaacttctcttttttttttttttttaaaaaaaaaactgtgttctgtatag

upper sequence: GRMZM2G059893_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT1G71410.1 (Arabidopsis thaliana), 5'ss of exon 13
---------------------------------------CACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtat-cat----ttatcctgcattgctctctacgtgtccatcaatatgtcaactaaactactacg--tatttctacag--------------------------
                                       | || |||||||| || ||||| |||||||| |||||||||||||||||||| |||   |||| | |||    |||||   || | || |  |   ||   |  |  |    || | |  | |     | | | ||  |                          
CAGAACATGTGCTTACCCTGATGATGCCGCTTCTCACTGCCCAACAACTGAACGTCCAACAGTTTGCCAAATATATGCTATTTGTCAAGGATATTCTCAGgtgtgcatcttgttatcagtcagtacttttgaatagtgttttcacgtccgtaccacaacagtgttgttgtctttattgtgatttgtattcatctattgtaacag

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), 49 (downstream exon)
Score: 133

CACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtatcattta ... atttctacagCAAGATTGAAGAGAAGCGTGGTGTGACTGTTACAGATAATGGGAACACAGAGGTAAAATCATCACCTTCATTGGCAAACGGGATCCATTCTGAACCTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

CACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtatcattta ... atttctacagCAAGATTGAAGAGAAGCGTGGTGTGACTGTTACAGATAATGGGAACACAGAGGTAAAATCATCACCTTCATTGGCAAACGGGATCCATTCTGAACCTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 186

CACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtatcattta ... atttctacagCAAGATTGAAGAGAAGCGTGGTGTGACTGTTACAGATAATGGGAACACAGAGGTAAAATCATCACCTTCATTGGCAAACGGGATCCATTCTGAACCTATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 111

CACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtatcattta ... atttctacagCAAGATTGAAGAGAAGCGTGGTGTGACTGTTACAGATAATGGGAACACAGAGGTAAAATCATCACCTTCATTGGCAAACGGGATCCATTCTGAACCTATG