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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacaactatgacccaaaaccgtttcttaatcctaacatgtttttgcaactcattagtgatctttggtgcagATGGTAGCTGATGTAACAATTGGGTTTGTAAAAGATGCAAAACATCACATCGACGTTCAAGGATTTAATGTATACCACATGAACCGTTTGATAAAG

Basic information

species Zea mays
transcript GRMZM2G161087_T01
intron # 11
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|76917044|gb|DV166651.1|DV166651
EST:     AGGTCACCTACAGGCCTGTGGCACCTAATGGACATCCGAAGGATTCAAAT                         ATGGTAGCTGATGTAACAATTGGGTTTGTAAAAGATGCAAAACATCACATC
genomic: AGGTCACCTACAGGCCTGTGGCACCTAATGGACATCCGAAGGATTCAAATgtaaacaact ... tttggtgcagATGGTAGCTGATGTAACAATTGGGTTTGTAAAAGATGCAAAACATCACATC




















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: 119

AAAAGAGATTGAACACCATAATATTGTGACTGACATGATGTTGAAGAAAGAGGTCACCTACAGGCCTGTGGCACCTAATGGACATCCGAAGGATTCAAATgtaaacaact ... tttggtgcagATGGTAGCTGATGTAACAATTGGGTTTGTAAAAGATGCAAAACATCACATCGACGTTCAAGGATTTAATGTATACCACATGAACCGTTTGATAAAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 67

AAAAGAGATTGAACACCATAATATTGTGACTGACATGATGTTGAAGAAAGAGGTCACCTACAGGCCTGTGGCACCTAATGGACATCCGAAGGATTCAAATgtaaacaact ... tttggtgcagATGGTAGCTGATGTAACAATTGGGTTTGTAAAAGATGCAAAACATCACATCGACGTTCAAGGATTTAATGTATACCACATGAACCGTTTGATAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 68

AAAAGAGATTGAACACCATAATATTGTGACTGACATGATGTTGAAGAAAGAGGTCACCTACAGGCCTGTGGCACCTAATGGACATCCGAAGGATTCAAATgtaaacaact ... tttggtgcagATGGTAGCTGATGTAACAATTGGGTTTGTAAAAGATGCAAAACATCACATCGACGTTCAAGGATTTAATGTATACCACATGAACCGTTTGATAAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 85

AAAAGAGATTGAACACCATAATATTGTGACTGACATGATGTTGAAGAAAGAGGTCACCTACAGGCCTGTGGCACCTAATGGACATCCGAAGGATTCAAATgtaaacaact ... tttggtgcagATGGTAGCTGATGTAACAATTGGGTTTGTAAAAGATGCAAAACATCACATCGACGTTCAAGGATTTAATGTATACCACATGAACCGTTTGATAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccgtttcttaatcctaacatgtttttgcaactcattagtgatctttggtgcagATGGTAGCTGATGTAACAATTGGGTTTGTAAAAGATGCAAAACATCACATCGACGTTCAAGGATTTAATGTATACCACATGAACCGTTTGATAAAG
             tcctaac  putative branch site (score: 85)
                                           tcttt  putative PPT
     tttcttaat  TA-rich tract