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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagattcatcagttccatatctaaacagctattactattctgggttggttccactcctcttcatttccgctgtcgttctatttacag

Basic information

species Oryza sativa
transcript LOC_Os08g33850.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g33850.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G152457_T04 (Zea mays), 5'ss of exon 8
GATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagattcatcagttccatatctaaacagctattactattctgggttggttccactcctcttcatttccgctgtcgttctatttacag
|||||||||||  || |||||    || |||||||||||||||||||||||||||||||||||||||| | ||   |||   |||||||||||||||||||||||| ||||||||||||||||| ||| | |||| |||||||| || || ||||||     ||| ||| |||||||||
GATTGATGTTGTAAACCAAATCCATGGCGTGCCTGTTGACTGGGCATTGGGTGCTTTCATTGTGCAGACGACGATGAACAGAACAGAgtactcagattcatcagtttcatatctaaacagctatgactctcctggcttggttccgcttctgttcatt---attgtggttgtatttacag

upper sequence: LOC_Os08g33850.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G152457_T05 (Zea mays), 5'ss of exon 7
GATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagattcatcagttccatatctaaacagctattactattctgggttggttccactcctcttcatttccgctgtcgttctatttacag----------------
|||||||||||  || |||||    || |||||||||||||||||||||||||||||||||||||||| | ||   |||   |||||||||||||||||||||||| ||||||||||||||||| ||| | |||| |||||||| || || ||||||     ||| ||| |||||||||                
GATTGATGTTGTAAACCAAATCCATGGCGTGCCTGTTGACTGGGCATTGGGTGCTTTCATTGTGCAGACGACGATGAACAGAACAGAgtactcagattcatcagtttcatatctaaacagctatgactctcctggcttggttccgcttctgttcatt---attgtggttgtatttacagcattgtccattctaag
















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|218485593|gb|FG957932.1|FG957932
EST:     GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGA                         CATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGGCGGTATACGACA
genomic: GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagat ... ctatttacagCATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
EST: gi|88847073|gb|CI001345.1|CI001345
EST:     GCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGA                         CATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
genomic: GCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagat ... ctatttacagCATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
EST: gi|88850574|gb|CI094839.1|CI094839
EST:     TTTCATTGTGCAGAAGGCGTCAAACCAGACAGA                         CATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
genomic: TTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagat ... ctatttacagCATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
EST: gi|38482258|gb|CF966306.1|CF966306
EST:     GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGA                         CATGCTCCATCCTGAGGGGGAGAAG
genomic: GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagat ... ctatttacagCATGCTCCATCCTGAGGGGGAGAAG
EST: gi|86418187|gb|CI032396.1|CI032396
EST:     GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGA                         CATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
genomic: GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagat ... ctatttacagCATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
EST: gi|87016732|gb|CI275734.1|CI275734
EST:     GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGA                         CATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
genomic: GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagat ... ctatttacagCATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
EST: gi|86902960|gb|CI312337.1|CI312337
EST:     GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGA                         CATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
genomic: GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagat ... ctatttacagCATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
EST: gi|157650330|gb|EX449964.1|EX449964
EST:     GACTGGGCATTGGGTACTTTCATTGTGCAGAAGGCGTCAAACCAGACAGA                         CATGCTCCATCCTGAGGGGGAGAAGATCTCGC
genomic: GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagat ... ctatttacagCATGCTCCATCCTGAGGGGGAGAAGATCTCGC
EST: gi|88247995|gb|CI247844.1|CI247844
EST:     GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGA                         CATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
genomic: GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagat ... ctatttacagCATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
EST: gi|87019097|gb|CI297298.1|CI297298
EST:     GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGA                         CATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGA
genomic: GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagat ... ctatttacagCATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGA
EST: gi|29688532|gb|CB684807.1|CB684807
EST:     GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGA                         CATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
genomic: GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagat ... ctatttacagCATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
EST: gi|88968855|gb|CI098948.1|CI098948
EST:     GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGCCAAACCAGACAGA                         CATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
genomic: GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagat ... ctatttacagCATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
EST: gi|88198776|gb|CI198626.1|CI198626
EST:     GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGA                         CATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
genomic: GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagat ... ctatttacagCATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
EST: gi|88962527|gb|CI097679.1|CI097679
EST:     TGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGA                         CATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
genomic: TGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagat ... ctatttacagCATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
EST: gi|25806604|gb|CA762565.1|CA762565
EST:     GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGA                         CATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA
genomic: GACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagat ... ctatttacagCATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACA

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 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 72 (downstream exon)
Score: 11

GATTGATGTTGCGAATCAAATTGGCGGTGTGCCTGTTGACTGGGCATTGGGTGCTTTCATTGTGCAGAAGGCGTCAAACCAGACAGAgtactcagat ... ctatttacagCATGCTCCATCCTGAGGGGGAGAAGATCTCGCCTGAAGACGGTATACGACATGGAGAAAGGCCGGTACATCATAACCAGGGTGAGACGATGAGCCTTGCG




<











<


<