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

CTCAGAGCCATGTCCACAGAATGTACTTCATGGGACCTAATACTTTCCGAGAGCCCTGGCATCTCCCCTACTCACCTCCTGATGCGATAATTGGAATTGTgtaagattaataatattagaaatatagagtagctaagtgccattcgagatttgtattactgttattcacttgacatgatgcaagaaaagttaatttgcag...

Basic information

species Zea mays
transcript GRMZM2G015291_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015291_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os04g10380.1 (Oryza sativa), 5'ss of exon 15
CTCAGAGCCATGTCCACAGAATGTACTTCATGGGACCTAATACTTTCCGAGAGCCCTGGCATCTCCCCTACTCACCTCCTGATGCGATAATTGGAATTGTgtaagattaataatattagaaatatagagtagctaagtgccattcgagatttgtattactgttattcacttgacatgatgcaagaaaagttaatttgcag----------
| || ||||||| ||||||||||||||||||||||||||| || ||||| || || ||||| || || |||||||| |||||||| ||||| ||||| ||||||||||     |  ||  ||| || | ||||  |||  || |     ||  |    ||  || | | |   ||  ||| ||  | | ||  | |  ||          
CACAAAGCCATGCCCACAGAATGTACTTCATGGGACCTAACACCTTCCGGGAACCTTGGCACCTTCCTTACTCACCCCCTGATGCTATAATCGGAATCGTgtaagatt-----ttctaagaatctacattagcagagtatcacttatagttatttcatctcataatgatt---cacaatgtaaatacattt--tctatagtaaaaagcta

upper sequence: GRMZM2G015291_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA11G04290.1 (Glycine max), 5'ss of exon 15
CTCAGAGCCATGTCCACAGAATGTACTTCATGGGACCTAATACTTTCCGAGAGCCCTGGCATCTCCCCTACTCACCTCCTGATGCGATAATTGGAATTGTgtaagattaataatat-tagaaatatagagtagctaagtgccattcgagat-ttgtattactgttattcacttgacatgatgcaagaaaagttaatttgcag-
|||| || ||||| |||||||||||||| ||||| |||||||||||  |||| ||||||||||| || |||||||||||  |||| |||||||  |||||||||||  ||    || |  || |||  |   |           ||  ||| |  |||| | |||||  |  ||      ||||    |  |  | |   || 
CTCAAAGTCATGTACACAGAATGTACTTTATGGGTCCTAATACTTTTAGAGAACCCTGGCATCTTCCTTACTCACCTCCCCATGCTATAATTGAGATTGTgtaagagaaactccatattcaattattcatgtgtatgtcatggatcctgatgtcatattgc-gttat--atgtggggctgtgcatttcatatgtagtcatagt

upper sequence: GRMZM2G015291_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA01G41140.1 (Glycine max), 5'ss of exon 15
CTCAGAGCCATGTCCACAGAATGTACTTCATGGGACCTAATACTTTCCGAGAGCCCTGGCATCTCCCCTACTCACCTCCTGATGCGATAATTGGAATTGTgtaagattaataatattagaaatatagagtagctaagtgccattcgagatttgtat--tactgttattcacttgacatgatgcaagaaaagttaatttgcag
|||| |||||||| |||||||||||||| |||||||||||||||||  |||| ||||||||||| || |||||||| ||  |||| |||||||  |||||||||||  ||  |  |    |||      ||  |   || |||  || | |  | |  || || | |  |  ||      || |    | | ||   |    
CTCAAAGCCATGTACACAGAATGTACTTTATGGGACCTAATACTTTTAGAGAACCCTGGCATCTTCCTTACTCACCCCCCCATGCTATAATTGAGATTGTgtaagagaaactacgtattcaattattcatacgtgcatgtcatg-gatactgatgtcatattgctttatatgtggggctgtggatattaggataccatatt-

upper sequence: GRMZM2G015291_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv02s0012g00460.t01 (Vitis vinifera), 5'ss of exon 15
CTCAGAGCCATGTCCACAGAATGTACTTCATGGGACCTAATACTTTCCGAGAGCCCTGGCATCTCCCCTACTCACCTCCTGATGCGATAATTGGAATTGTgtaagat--taataatattagaaatatagagtagctaagtgc-cattcgagatttgtattactgttattcacttgacatgatgcaagaaaagttaatttgcag
|||||||||||||  |||| |||||||| ||||| || ||||||||| |||| ||||||||||| || ||||| |||||  |||| || || |  ||||||||||||   |||   | |  ||   ||   |  || |  || || | |     |   ||  ||||||    ||       | ||| |    |  ||||    
CTCAGAGCCATGTTTACAGGATGTACTTTATGGGTCCCAATACTTTCAGAGAACCCTGGCATCTTCCTTACTCTCCTCCCAATGCAATCATAGAGATTGTgtaagatagcaatttaacttaaagggtactttgactgatggcacaattggatgctaggtttatgttatgatattatgggtttacaatatggctggatttc---

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), 49 (downstream exon)
Score: 107

CTCAGAGCCATGTCCACAGAATGTACTTCATGGGACCTAATACTTTCCGAGAGCCCTGGCATCTCCCCTACTCACCTCCTGATGCGATAATTGGAATTGTgtaagattaa ... ttcctttcagTTATGAAGATGCTTTCAACCGTTTTATTGATGAGATCAATTTGGTGGCTGCATATGAGTGGTGGGAAGGATCTATACATAGTATACTTTCTGTTCTTGCG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 121

CTCAGAGCCATGTCCACAGAATGTACTTCATGGGACCTAATACTTTCCGAGAGCCCTGGCATCTCCCCTACTCACCTCCTGATGCGATAATTGGAATTGTgtaagattaa ... ttcctttcagTTATGAAGATGCTTTCAACCGTTTTATTGATGAGATCAATTTGGTGGCTGCATATGAGTGGTGGGAAGGATCTATACATAGTATACTTTCTGTTCTTGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

CTCAGAGCCATGTCCACAGAATGTACTTCATGGGACCTAATACTTTCCGAGAGCCCTGGCATCTCCCCTACTCACCTCCTGATGCGATAATTGGAATTGTgtaagattaa ... ttcctttcagTTATGAAGATGCTTTCAACCGTTTTATTGATGAGATCAATTTGGTGGCTGCATATGAGTGGTGGGAAGGATCTATACATAGTATACTTTCTGTTCTTGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

CTCAGAGCCATGTCCACAGAATGTACTTCATGGGACCTAATACTTTCCGAGAGCCCTGGCATCTCCCCTACTCACCTCCTGATGCGATAATTGGAATTGTgtaagattaa ... ttcctttcagTTATGAAGATGCTTTCAACCGTTTTATTGATGAGATCAATTTGGTGGCTGCATATGAGTGGTGGGAAGGATCTATACATAGTATACTTTCTGTTCTTGCG