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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCCgtatgatcttctgctacttttcaaatgcacaccattattcctttcctatttagtaatttcttttgatgttttaaaacgctgatgagttataacaaggtga...

Basic information

species Zea mays
transcript GRMZM2G344924_T01
intron # 7
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|31358918|gb|CD443275.1|CD443275
EST:     GGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCC                         AACTCCTACCCTGTCCAGTATGG
genomic: GGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCCgtatgatctt ... ttttacccagAACTCCTACCCTGTCCAGTATGG
EST: gi|20507629|gb|BQ279708.1|BQ279708
EST:     GGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCC                         AACTCCTACCCTGTCCAGTATGGTCATGCAGCCTGCTCCTGTTTCAAATCC
genomic: GGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCCgtatgatctt ... ttttacccagAACTCCTACCCTGTCCAGTATGGTCATGCAGCCTGCTCCTGTTTCAAATCC
EST: gi|78116408|gb|DV534795.1|DV534795
EST:     GGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCC                         AACTCCTACCCTGTCCAGTATGGTCATGCAGCCTGCTCCTGTTTCAAATCC
genomic: GGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCCgtatgatctt ... ttttacccagAACTCCTACCCTGTCCAGTATGGTCATGCAGCCTGCTCCTGTTTCAAATCC
EST: gi|26456661|gb|CA828244.1|CA828244
EST:     GGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCC                         AACTCCTACCCTGTCCAGTATGGTCATGCAGCCTGCTCCTGTTTCAAATCC
genomic: GGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCCgtatgatctt ... ttttacccagAACTCCTACCCTGTCCAGTATGGTCATGCAGCCTGCTCCTGTTTCAAATCC

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), 49 (downstream exon)
Score: 316

CTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCCgtatgatctt ... ttttacccagAACTCCTACCCTGTCCAGTATGGTCATGCAGCCTGCTCCTGTTTCAAATCCATTTGGGATGCTTCCAGCAATGCCTCACATGTCCATTGGAAATGGTGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

CTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCCgtatgatctt ... ttttacccagAACTCCTACCCTGTCCAGTATGGTCATGCAGCCTGCTCCTGTTTCAAATCCATTTGGGATGCTTCCAGCAATGCCTCACATGTCCATTGGAAATGGTGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

CTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCCgtatgatctt ... ttttacccagAACTCCTACCCTGTCCAGTATGGTCATGCAGCCTGCTCCTGTTTCAAATCCATTTGGGATGCTTCCAGCAATGCCTCACATGTCCATTGGAAATGGTGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

CTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCCgtatgatctt ... ttttacccagAACTCCTACCCTGTCCAGTATGGTCATGCAGCCTGCTCCTGTTTCAAATCCATTTGGGATGCTTCCAGCAATGCCTCACATGTCCATTGGAAATGGTGGA