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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgaccaatcttgtgtactgctgaagctgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcag

Basic information

species Oryza sativa
transcript LOC_Os04g32330.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM5G807639_T02 (Zea mays), 5'ss of exon 10
GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgaccaatcttgtgtactgctgaagctgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcag
||| |||||||||||||| || ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| ||||| |||||||||||||||||    | |||| |||  |||  |||||          |||  ||   |||  || |||       |||  ||  ||||  ||||    
GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTCAAATTGGGTCTTATGTCTTGCTTTGtcaaggtact---tagtcttatgtgttgc-aaagct---------tttg--aaccatac--atttatatggctggctaattttatttattttg----

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM5G807639_T03 (Zea mays), 5'ss of exon 10
GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgaccaatcttgtgtactgctgaagctgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcag
||| |||||||||||||| || ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| ||||| |||||||||||||||||    | |||| |||  |||  |||||          |||  ||   |||  || |||       |||  ||  ||||  ||||||||
GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTCAAATTGGGTCTTATGTCTTGCTTTGTCAAGgtact---tagtcttatgtgttgc-aaagct---------tttg--aaccatac--atttatatggctggctaattttatttattttgtcag

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G079538_T02 (Zea mays), 5'ss of exon 11
GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgaccaatcttgtgtactgctgaagctgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcag
||| |||||||||||||| || ||||||||||| ||||| |||||||| ||||| ||||| ||||||||||| ||||| ||||||||||||||| |  ||| ||||  |   |||  |       || ||||    || |||||        |       |||  ||  ||||| ||||  ||
GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAGgtatttgccagtcttaggcgttgcaaag------cttttgcaccatactttta--------tgtggctggctaattatatttgttttggtag

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA02G46200.1 (Glycine max), 5'ss of exon 12
GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgaccaatcttgtgtactgctgaagc-tgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcag
|||||||||||||||||| || ||||||||||||||||  |||||    ||||| || ||||||||||| || |||||  |||||||||| |||        | || |  | | |||||   | |||||  ||| ||   |||  |   |   |||    | ||  ||    |  |  ||| ||
GACTAATTTGATGAAGCTCCGTTCTGATTATAAGGATGCTTTTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTCAAAgtat------gttttcta-attactgaaatataaacta--gctgggc--tttctcctttgatttcctcatactttttatggtctccatgttag

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA14G02530.1 (Glycine max), 5'ss of exon 12
GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgaccaatcttgtgtactgctgaagc-tgaactattgcttggtaattttactaatatattca-atgtgctcgttccatttgctttgtcag
|||||||||||||||||| || ||||||||||||||||  |||||    ||||| || ||||||||||| || |||||  ||||||| || |||        | || |  | | ||||||  |  ||||  ||| |||  | |   |   |||| |  ||   ||  ||    |  |  ||| ||
GACTAATTTGATGAAGCTCCGTTCTGATTATAAGGATGCTTTTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTGAAAgtat------gttttcta-attactgaagtatagacta--gctgggttttctctttttgatatcctcatacactttttatggtctccatgttag

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|38478516|gb|CF962649.1|CF962649
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
EST: gi|55436812|gb|CV731566.1|CV731566
EST:     ACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
genomic: ACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
EST: gi|33794308|gb|CF323041.1|CF323041
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
EST: gi|58613350|gb|CK041062.1|CK041062
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGGCAGG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
EST: gi|25806798|gb|CA762759.1|CA762759
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
EST: gi|11233501|gb|AU164913.1|AU164913
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
EST: gi|5701685|gb|AU062775.2|AU062775
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
EST: gi|55435262|gb|CV730762.1|CV730762
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
EST: gi|5443721|gb|AU062434.2|AU062434
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTG
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTG
EST: gi|58609985|gb|CK038018.1|CK038018
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAGGGCTGTCATTGAT
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT

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: 69 (upstream exon), 72 (downstream exon)
Score: 70

GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG




<











<


<