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

GATCGTCATCGACAACGAGTCCTCGGCGGAGGCCACAATTGTAAGGgtatgttccttgctccggttaatttgctgaactgaatttaatttccgctgtcgattttgggaatttaccattctgctgttttctccatggtattgcattatgatttgtag

Basic information

species Zea mays
transcript GRMZM2G383408_T01
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|149084763|gb|EE174260.2|EE174260
EST:     GATCGTCATCGACAACGAGTCCTCGGCGGAGGCCACAATTGTAAGG                         GTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATG
genomic: GATCGTCATCGACAACGAGTCCTCGGCGGAGGCCACAATTGTAAGGgtatgttcct ... tgatttgtagGTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATG
EST: gi|22489287|gb|BU049210.1|BU049210
EST:     CGAGTCCTCGGCGGAGGCCACAATTGTAAGG                         GTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATG
genomic: CGAGTCCTCGGCGGAGGCCACAATTGTAAGGgtatgttcct ... tgatttgtagGTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATG
EST: gi|89106281|gb|DY576498.1|DY576498
EST:     CGAGTCCTCGGCGGAGGCCACAATTGTAAGG                         GTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATG
genomic: CGAGTCCTCGGCGGAGGCCACAATTGTAAGGgtatgttcct ... tgatttgtagGTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATG
EST: gi|148947740|gb|EC893223.2|EC893223
EST:     GATCGTCATCGACAACGAGTCCTCGGCGGAGGCCACAATTGTAAGG                         GTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATG
genomic: GATCGTCATCGACAACGAGTCCTCGGCGGAGGCCACAATTGTAAGGgtatgttcct ... tgatttgtagGTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATG
EST: gi|18053160|gb|BM318818.1|BM318818
EST:     CGAGTCCTCGGCGGAGGCCACAATTGTAAGG                         GTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATG
genomic: CGAGTCCTCGGCGGAGGCCACAATTGTAAGGgtatgttcct ... tgatttgtagGTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATG
EST: gi|91870307|gb|EB400808.1|EB400808
EST:     GATCGTCATCGACAACGAGTCCTCGGCGGAGGCCACAATTGTAAGG                         GTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATG
genomic: GATCGTCATCGACAACGAGTCCTCGGCGGAGGCCACAATTGTAAGGgtatgttcct ... tgatttgtagGTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATG
EST: gi|8367862|gb|BE050807.1|BE050807
EST:     GATCGTCATCGACAACGAGTCCTCGGCGGAGGCCACAATTGTAAGG                         GTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATG
genomic: GATCGTCATCGACAACGAGTCCTCGGCGGAGGCCACAATTGTAAGGgtatgttcct ... tgatttgtagGTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATG

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: 46 (upstream exon), 49 (downstream exon)
Score: 152

GATCGTCATCGACAACGAGTCCTCGGCGGAGGCCACAATTGTAAGGgtatgttcct ... tgatttgtagGTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATGATTGATCTCAACCTTGTCATAGGCAAGGCATATATAACCTCGGATGGTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 156

GATCGTCATCGACAACGAGTCCTCGGCGGAGGCCACAATTGTAAGGgtatgttcct ... tgatttgtagGTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATGATTGATCTCAACCTTGTCATAGGCAAGGCATATATAACCTCGGATGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 282

GATCGTCATCGACAACGAGTCCTCGGCGGAGGCCACAATTGTAAGGgtatgttcct ... tgatttgtagGTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATGATTGATCTCAACCTTGTCATAGGCAAGGCATATATAACCTCGGATGGTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 273

GATCGTCATCGACAACGAGTCCTCGGCGGAGGCCACAATTGTAAGGgtatgttcct ... tgatttgtagGTAGATAGCGCGAATGAATACGGGATATTGCTGGAAGTGATCCAGGTCATGATTGATCTCAACCTTGTCATAGGCAAGGCATATATAACCTCGGATGGTG