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'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAAGGAGGACTCCTAAATGCTGTAGAGACTGTTTTGAAACTCTCATTACCAAATGTTTACCTGTGGCTTTGCATGTTCTATGCTTTTTTCCATCTCTGgtaatttccattttctacttattcataatcaagaaaatggtcactattagactataatatattcaaaatcaatttatttctgaatgcatacatttccttgcatgatccaagcttgtgaacaaataatttctctaacaccagacttacagtttaaacattgataattgcacag

Basic information

species Oryza sativa
transcript LOC_Os05g10810.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g10810.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G130749_T01 (Zea mays), 5'ss of exon 9
TGAAAGGAGGACTCCTAAATGCTGTAGAGACTGTTTTGAAACTCTCATTACCAAATGTTTACCTGTGGCTTTGCATGTTCTATGCTTTTTTCCATCTCTGgtaat---ttccattttctacttattcat----aatcaagaaaatggtcactattag-actataata-tattcaaaatcaat-ttatttctgaatgcatacatttccttgcatgatccaagcttgtgaacaaataatttctctaacac-cagacttacagttt-aaacattgat--aattgcacag
|||  |||||| | || ||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||| |||    |||||||||| ||||| |   ||  ||||||||  |||||||    | ||||  | ||| ||  |  |   | |||  || |||     ||| ||  |  ||||     ||| |||   || | |  |   ||   | |      ||  | | || ||    || | || ||||||  ||| |  ||  |  |  ||||
TGATGGGAGGATTACTGAATGCTGTAGAGACTGTTTTGAAGCTCTCATTACCAAATGTCTACCTGTGGCTTTGCATGTTTTATTGCCTTTTCCATCTGTGgtagtaaattatattttctatctattcattcaaattcaaatacatgatcgatcctgatattattctaatatcagtcatcgatgcttcttctccgaacatgcatgctctcggagaa---aattatttccttttatgctctttcaaatttgcatatttgcagtttcgaacttatattcatctatacag
















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|29664361|gb|CB660636.1|CB660636
EST:     CCAAATGTTTACCTGTGGCTTTGCATGTTCTATGCTTTTTTCCATCTCTG                         GTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAA
genomic: CCAAATGTTTACCTGTGGCTTTGCATGTTCTATGCTTTTTTCCATCTCTGgtaatttcca ... aattgcacagGTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAA
EST: gi|29641508|gb|CB646515.1|CB646515
EST:     GCTTTTTTCCATCTCTG                         GTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAA
genomic: GCTTTTTTCCATCTCTGgtaatttcca ... aattgcacagGTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAA
EST: gi|29646483|gb|CB651490.1|CB651490
EST:     CCAAATGTTTACCTGTGGCTTTGCATGTTCTATGCTTTTTTCCATCTCTG                         GTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAA
genomic: CCAAATGTTTACCTGTGGCTTTGCATGTTCTATGCTTTTTTCCATCTCTGgtaatttcca ... aattgcacagGTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAA
EST: gi|29664324|gb|CB660599.1|CB660599
EST:     CCAAATGTTTACCTGTGGCTTTGCATGTTCTATGCTTTTTTCCATCTCTG                         GTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAA
genomic: CCAAATGTTTACCTGTGGCTTTGCATGTTCTATGCTTTTTTCCATCTCTGgtaatttcca ... aattgcacagGTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAA
EST: gi|29646484|gb|CB651491.1|CB651491
EST:     ATGCTTTTTTCCATCTCTG                         GTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAA
genomic: ATGCTTTTTTCCATCTCTGgtaatttcca ... aattgcacagGTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAA
EST: gi|29614065|gb|CB619078.1|CB619078
EST:     CCAAATGTTTACCTGTGGCTTTGCATGTTCTATGCTTTTTTCCATCTCTG                         GTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAA
genomic: CCAAATGTTTACCTGTGGCTTTGCATGTTCTATGCTTTTTTCCATCTCTGgtaatttcca ... aattgcacagGTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAA

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: 64 (upstream exon), 60 (downstream exon)
Score: 13

TGAAAGGAGGACTCCTAAATGCTGTAGAGACTGTTTTGAAACTCTCATTACCAAATGTTTACCTGTGGCTTTGCATGTTCTATGCTTTTTTCCATCTCTGgtaatttcca ... aattgcacagGTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAG




<











<


<