Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAGgtacagttacttctgagtttgtagttttggctggtttgcacctatctaattcttgcacttgcttgtgtag

Basic information

species Zea mays
transcript GRMZM2G118467_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118467_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g27230.1 (Oryza sativa), 5'ss of exon 5
GTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAGgtacagttacttctgagtttgtagttttg-gctggtttgcac-------ctatctaa---ttcttgcacttgcttgtgtag
|| ||| |||||  ||||   ||||| ||||| ||||| || ||||| ||||||||||| |||||||| ||||||||||| ||||||| |  ||| |||| ||   |||  |  |||  | ||||        ||||||||   |||||| || || ||||  ||
GTATATACTGGAGCTCCTCATGCCATCGATGGCTGTGCCACCTTTTTCCGTAGAGACAAATTTTCACACGTTAAAAAATATGAGgtacggccactgctgatttgagagtggtatgctaatctgcaggctgcagctatctaatatttcttgtacctggttgttcag

upper sequence: GRMZM2G118467_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA09G15980.2 (Glycine max), 5'ss of exon 4
GTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAGgt--acagttacttctgagtttg-tagttttggctggtttgcacctatctaattcttgcacttgcttgtgtag--
|||||   ||| ||  | |   | || ||||| ||||| || ||||| ||||||||||  |||||||||||||| |||||||||||    | ||  ||  |  | || |||||       ||||| ||  |  | |   |      ||||||  |    
GTGTACAGTGGCAACACAAATACAATTGATGGGTGTGCAACATTTTTCCGTAGAGACAGATTTTCACATGTTAAGAAATACGAGgttgggaattgatttggcatatggtagttcaattatgtttgtacacaaattagaatgatgtgtgcttgcatgcag

upper sequence: GRMZM2G118467_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA02G26620.2 (Glycine max), 5'ss of exon 4
GTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAGgt--acagttacttctgagtttg-tagttttggctggtttgcacctatctaattcttgcacttgcttgtgtag--
|||||   ||| ||  | |   | || ||||| ||||| || ||||| ||||||||||  |||||||||||||| ||||| |||||    | ||  ||  |  | || |||||       ||||| ||  |  | |   |      ||||||  |    
GTGTACAGTGGCAACACAAATACAATTGATGGGTGTGCAACATTTTTCCGTAGAGACAGATTTTCACATGTTAAGAAATATGAGgttgggaattgatttggcatatggtagttcaattatgtttgtacacaaattagaatgatgtgtgcttgcatgcag

upper sequence: GRMZM2G118467_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G36550.1 (Glycine max), 5'ss of exon 4
GTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAGgt--acagttacttc-tgagtttg-tagttttggctggtttgcacctatctaattcttgcacttgcttgtgtag--
|| ||   ||||||   ||   | || ||||| ||||| || ||||| ||||||||||  ||||||||||| |||||||| |||||    | ||  ||  || || ||  |||| |     ||||| ||  | |  |   |      || |||  |    
GTATACAATGGAAACATTAATACAATTGATGGGTGTGCAACATTTTTCCGTAGAGACAGATTTTCACATGTGAAAAAATATGAGgttggaaattgttttatgtgtatgacagttctcttaagtttgtacacaacatagagtgatgtctgtttgcatgcag

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), 48 (downstream exon)
Score: 151

GTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAGgtacagttac ... gcttgtgtagGTTGAGTTCAATAAGGCTGCACAGTCTTTAACAGATGCTATTATTCCTGCTGCCCAGAAAAGAGTGGCTTTAAGTCGATTGATTAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 101

GTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAGgtacagttac ... gcttgtgtagGTTGAGTTCAATAAGGCTGCACAGTCTTTAACAGATGCTATTATTCCTGCTGCCCAGAAAAGAGTGGCTTTAAGTCGATTGATTAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 138

GTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAGgtacagttac ... gcttgtgtagGTTGAGTTCAATAAGGCTGCACAGTCTTTAACAGATGCTATTATTCCTGCTGCCCAGAAAAGAGTGGCTTTAAGTCGATTGATTAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

GTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAGgtacagttac ... gcttgtgtagGTTGAGTTCAATAAGGCTGCACAGTCTTTAACAGATGCTATTATTCCTGCTGCCCAGAAAAGAGTGGCTTTAAGTCGATTGATTAAA