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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgctgaataataggcacacttttttatttgaaacccttgtgcctcacatcgttgactgacccaggtatttgtttatgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTGCTGGCGTCTGTTCTGGTTTGTGTTGTGCTTTGTGTCTTATCTTCCGAAG

Basic information

species Zea mays
transcript GRMZM2G118014_T04
intron # 13
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|76286405|gb|DV025973.1|DV025973
EST:     GAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
genomic: GAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
EST: gi|211519312|gb|FL433830.1|FL433830
EST:     GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
genomic: GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
EST: gi|76286406|gb|DV025974.1|DV025974
EST:     GAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
genomic: GAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
EST: gi|161588478|gb|EY959060.1|EY959060
EST:     GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAG
genomic: GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAG
EST: gi|149086754|gb|EE176294.2|EE176294
EST:     GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
genomic: GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
EST: gi|24767722|gb|CA402862.1|CA402862
EST:     GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
genomic: GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
EST: gi|211168469|gb|FK981061.1|FK981061
EST:     GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
genomic: GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG

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), 49 (downstream exon)
Score: 244

GGGACCGTCGCCATGACCGCGACCGGGATAGGGATTATGACCGCTCCCGCGGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTGCTGGCGTCTGTTCTGGTTTGTGTTGTGCTTTGTGTCTTATCTTCCGAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 69

GGGACCGTCGCCATGACCGCGACCGGGATAGGGATTATGACCGCTCCCGCGGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTGCTGGCGTCTGTTCTGGTTTGTGTTGTGCTTTGTGTCTTATCTTCCGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 66

GGGACCGTCGCCATGACCGCGACCGGGATAGGGATTATGACCGCTCCCGCGGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTGCTGGCGTCTGTTCTGGTTTGTGTTGTGCTTTGTGTCTTATCTTCCGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

GGGACCGTCGCCATGACCGCGACCGGGATAGGGATTATGACCGCTCCCGCGGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTGCTGGCGTCTGTTCTGGTTTGTGTTGTGCTTTGTGTCTTATCTTCCGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaacccttgtgcctcacatcgttgactgacccaggtatttgtttatgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTGCTGGCGTCTGTTCTGGTTTGTGTTGTGCTTTGTGTCTTATCTTCCGAAG
                        gactgac  putative branch site (score: 112)
                                    tatttgtttatgattt  TA-rich tract