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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACTGATGATTGCGGCGGTTCCGAACGTCATGGGCTGGCTCGCGATCTCCCTGGCAAGGgtatgtcgctagtcgctactacgtgtgtcggtttatctccactcgttgtcttcacagatgacagcatcggctttgatggccgtcaatgtctgctctgctctgcag

Basic information

species Zea mays
transcript GRMZM2G098679_T02
intron # 3
splice site 5'
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|148953879|gb|EC899257.2|EC899257
EST:     TTGCGGCGGTTCCGAACGTCATGGGCTGGCTCGCGATCTCCCTGGCAAGG                         GACACTTCGTTTCTGTACGTGGGGAGGTTGCTGGAAGGATTCGGTGTCGGC
genomic: TTGCGGCGGTTCCGAACGTCATGGGCTGGCTCGCGATCTCCCTGGCAAGGgtatgtcgct ... tgctctgcagGACACTTCGTTTCTGTACGTGGGGAGGTTGCTGGAAGGATTCGGTGTCGGC
EST: gi|149102088|gb|EE188063.2|EE188063
EST:     TTGCGGCGGTTCCGAACGTCATGGGCTGGCTCGCGATCTCCCTGGCAAGG                         GACACTTCGTTTCTGTACGTGGGGAGGTTGCTGGAAGGATTCGGTGTCGGC
genomic: TTGCGGCGGTTCCGAACGTCATGGGCTGGCTCGCGATCTCCCTGGCAAGGgtatgtcgct ... tgctctgcagGACACTTCGTTTCTGTACGTGGGGAGGTTGCTGGAAGGATTCGGTGTCGGC

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: 42 (upstream exon), 21 (downstream exon)
Score: 4

TCACTGATGATTGCGGCGGTTCCGAACGTCATGGGCTGGCTCGCGATCTCCCTGGCAAGGgtatgtcgct ... tgctctgcagGACACTTCGTTTCTGTACGTGGGGAGGTTGCTGGAAGGATTCGGTGTCGGCGTCATCTCCTACGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 149

TCACTGATGATTGCGGCGGTTCCGAACGTCATGGGCTGGCTCGCGATCTCCCTGGCAAGGgtatgtcgct ... tgctctgcagGACACTTCGTTTCTGTACGTGGGGAGGTTGCTGGAAGGATTCGGTGTCGGCGTCATCTCCTACGTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 135

TCACTGATGATTGCGGCGGTTCCGAACGTCATGGGCTGGCTCGCGATCTCCCTGGCAAGGgtatgtcgct ... tgctctgcagGACACTTCGTTTCTGTACGTGGGGAGGTTGCTGGAAGGATTCGGTGTCGGCGTCATCTCCTACGTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 79

TCACTGATGATTGCGGCGGTTCCGAACGTCATGGGCTGGCTCGCGATCTCCCTGGCAAGGgtatgtcgct ... tgctctgcagGACACTTCGTTTCTGTACGTGGGGAGGTTGCTGGAAGGATTCGGTGTCGGCGTCATCTCCTACGTG