Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTGCGTCAGCAGATGCCTGACGGGTGGAGATTTGGGAGAATCCCAGTGATTCTGTGAATCCTTTTTGTTCTCTGCTTCGTCGGTTCGGGGTTTTAAGgtttttgcgctcaatttcttccctgcagttcactttgggcactaatggttgctgctgtctagtcactgaaactctactttgcggtaggttcgtttcagat...

Basic information

species Zea mays
transcript GRMZM2G020484_T08
intron # 1
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|149106098|gb|EE291762.2|EE291762
EST:     GATTCTGTGAATCCTTTTTGTTCTCTGCTTCGTCGGTTCGGGGTTTTAAG                         GGCAGGAGAGGAGGCCACTCTGACTGTCACTCTTAGCTTCGCGTCACCTGA
genomic: GATTCTGTGAATCCTTTTTGTTCTCTGCTTCGTCGGTTCGGGGTTTTAAGgtttttgcgc ... gtatttgcagGGCAGGAGAGGAGGCCACTCTGACTGTCACTCTGAGCTTCGCGTCACCTGA
EST: gi|78112564|gb|DV530958.1|DV530958
EST:     GATTCTGTGAATCCTTTTTGTTCTCTGCTTCGTCGGTTCGGGGTTTTAAG                         GGCAGGAGAGGAGGCCACTCTGACTGTCACTCTGAGCTTCACGTCACCTGA
genomic: GATTCTGTGAATCCTTTTTGTTCTCTGCTTCGTCGGTTCGGGGTTTTAAGgtttttgcgc ... gtatttgcagGGCAGGAGAGGAGGCCACTCTGACTGTCACTCTGAGCTTCGCGTCACCTGA

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 3 RNA-Seq libraries.


Block sizes: 20 (upstream exon), 30 (downstream exon)
Score: 1

CTTCTGCGTCAGCAGATGCCTGACGGGTGGAGATTTGGGAGAATCCCAGTGATTCTGTGAATCCTTTTTGTTCTCTGCTTCGTCGGTTCGGGGTTTTAAGgtttttgcgc ... gtatttgcagGGCAGGAGAGGAGGCCACTCTGACTGTCACTCTGAGCTTCGCGTCACCTGAGTACTGACGGACGACATGGGAGAAGTTGAGGACATGTACACCCAAGACG


Block sizes: 33 (upstream exon), 38 (downstream exon)
Score: 2

CTTCTGCGTCAGCAGATGCCTGACGGGTGGAGATTTGGGAGAATCCCAGTGATTCTGTGAATCCTTTTTGTTCTCTGCTTCGTCGGTTCGGGGTTTTAAGgtttttgcgc ... gtatttgcagGGCAGGAGAGGAGGCCACTCTGACTGTCACTCTGAGCTTCGCGTCACCTGAGTACTGACGGACGACATGGGAGAAGTTGAGGACATGTACACCCAAGACG


Block sizes: 9 (upstream exon), 41 (downstream exon)
Score: 1

CTTCTGCGTCAGCAGATGCCTGACGGGTGGAGATTTGGGAGAATCCCAGTGATTCTGTGAATCCTTTTTGTTCTCTGCTTCGTCGGTTCGGGGTTTTAAGgtttttgcgc ... gtatttgcagGGCAGGAGAGGAGGCCACTCTGACTGTCACTCTGAGCTTCGCGTCACCTGAGTACTGACGGACGACATGGGAGAAGTTGAGGACATGTACACCCAAGACG