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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacaaattggattttggaacggaggcagtaatatctaattctgtatttattattttctattttgtataactatttcattgttcattctgttttgtttcagATACGAGGCATGCACACAATAATAAGGGATGCTGCCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTGGTCAGTATATAAATGT

Basic information

species Zea mays
transcript GRMZM2G169462_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169462_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 8
-------------------------------------------tacaaattggattttggaacggaggcagtaatatctaattctgtatttatta------ttttctattttgtataactatttcattgttcattctgttttgtttcagATACGAGGCATGCACACAATAATAAGGGATGCTGCCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTGGTCAGTATATAAATGT
                                            ||  ||||  |||||  |       | || |   |  |  || | |||||       |||| ||   | ||||| ||||    | |  |||||  ||| |||||||||||||| ||||||||||||||| |||||||||||||| ||||||||||||||||||| ||||||||||||||||||||||||                
gtacttcatgtgaccataaatgtgctgcagttttttcttataaaaccgattgttttttgataatctcataatattgaatgttaatgcaattatttctggatttttgtagcgtatataaatattagcatttcaattcttctttctttcagATACGAGGTATGCACACAATAATACGGGATGCTGCCACAACAACACATGATTTCATATTCTATGCTGATCGGTTGATTCGATTG----------------

upper sequence: GRMZM2G169462_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 8
----------------------------------------------tacaaat-tggattttggaacggaggcagtaatatctaattctgtatttattattttctattttgtataac-tatttcattgtt--catt------ctgttttgtttcagATACGAGGCATGCACACAATAATAAGGGATGCTGCCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTGGTCAGTATATAAATGT
                                               |||| | |   | ||   |  |   || ||||||  |||    |||  | | |||     ||| | |||| ||| | | | ||  ||||      ||| ||| |||||||||||||| ||||||||||||||| | |||||||||||| ||||||||||||||||||| ||||| ||||||||||||||||||                
gtacctgatgtaaccataaatgttctgcagtcttttcttatataagaacaattgtctgtcttttgatagtctca-taatattgaatgtaatatgcactttttcaggatttttgtaacatatataaatattgacattgcaatgctgctttctttcagATACGAGGTATGCACACAATAATACGCGATGCTGCCACAACAACACATGATTTCATATTCTATGCCGATCGGTTGATTCGATTG----------------
















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), 48 (downstream exon)
Score: 87

GGCAATTGACCTAATCGTTCAGCATATTCGGACTAAACTTGGACAACATGATCTTCGTAAAATACACCCTAATCTGTATGTAATTCAGACTACTTATCAGgtacctaatg ... tttgtttcagATACGAGGCATGCACACAATAATAAGGGATGCTGCCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTGGTCAGTATATAAATGT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 109

GGCAATTGACCTAATCGTTCAGCATATTCGGACTAAACTTGGACAACATGATCTTCGTAAAATACACCCTAATCTGTATGTAATTCAGACTACTTATCAGgtacctaatg ... tttgtttcagATACGAGGCATGCACACAATAATAAGGGATGCTGCCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTGGTCAGTATATAAATGT


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 86

GGCAATTGACCTAATCGTTCAGCATATTCGGACTAAACTTGGACAACATGATCTTCGTAAAATACACCCTAATCTGTATGTAATTCAGACTACTTATCAGgtacctaatg ... tttgtttcagATACGAGGCATGCACACAATAATAAGGGATGCTGCCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTGGTCAGTATATAAATGT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 175

GGCAATTGACCTAATCGTTCAGCATATTCGGACTAAACTTGGACAACATGATCTTCGTAAAATACACCCTAATCTGTATGTAATTCAGACTACTTATCAGgtacctaatg ... tttgtttcagATACGAGGCATGCACACAATAATAAGGGATGCTGCCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTGGTCAGTATATAAATGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattattttctattttgtataactatttcattgttcattctgttttgtttcagATACGAGGCATGCACACAATAATAAGGGATGCTGCCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTGGTCAGTATATAAATGT
                  gtataac  putative branch site (score: 175)
                                       ttctgttttgtttc  putative PPT
     tattttctattttgta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacaaattggattttggaacggaggcagtaatatctaattctgtatttattattttctattttgtataactatttcattgttcattctgttttgtttcagATACGAGGCATGCACACAATAATAAGGGATGCTGCCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTGGTCAGTATATAAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT