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'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGGATGATACTTGCTCATTTATGTGATGAACCCAAAGGTCTCAAAACTGGAATGTGCATGgtatgtccatactccatagttccatgtcttgtttctatctgcacatcacgtgtacatgagtcacttgaagtaaaataccaaatatctcttatttcag

Basic information

species Oryza sativa
transcript LOC_Os06g10280.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g10280.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G701058_T01 (Zea mays), 5'ss of exon 12
GGAAGGATGATACTTGCTCATTTATGTGATGAACCCAAAGGTCTCAAAACTGGAATGTGCATGgtatgtccatactccatagttccatgtcttgtttctatctgcacatcacgtgtacatgagtcacttgaagtaaaataccaaatatctcttatttcag
||||| ||||||||||||||||| |||||||||||||||||||| ||| |||| |||| |||||||||     |||    |||  | |||    ||   ||||  | ||  |  ||  | |   |  || |||         ||| | ||||||||||||
GGAAGAATGATACTTGCTCATTTGTGTGATGAACCCAAAGGTCTAAAATCTGGGATGTTCATGgtatg-----actttgaagtgtcctgt---attctcatctttagatgccaagtgtaggctactattaaagcgctgacaaaaaaaactcttatttcag

upper sequence: LOC_Os06g10280.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G701058_T02 (Zea mays), 5'ss of exon 1
-------------------------------------GGAAGGATGATACTTGCTCATTTATGTGATGAACCCAAAGGTCTCAAAACTGGAATGTGCATGgtatgtccatactccatagttccatgtcttgtttctatctgcacatcacgtgtacatgagtcacttgaagtaaaataccaaatatctcttatttcag
                                     ||||| ||||||||||||||||| |||||||||||||||||||| ||| |||| |||| |||||||||     |||    |||  | |||    ||   ||||  | ||  |  ||  | |   |  || |||         ||| | ||||||||||||
ACTACTGCTTATAATGTAAATAATCATCTATGAACAGGGAAGAATGATACTTGCTCATTTGTGTGATGAACCCAAAGGTCTAAAATCTGGGATGTTCATGgtatg-----actttgaagtgtcctgt---attctcatctttagatgccaagtgtaggctactattaaagcgctgacaaaaaaaactcttatttcag

upper sequence: LOC_Os06g10280.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA02G14210.1 (Glycine max), 5'ss of exon 15
GGAAGGATGATACTTGCTCATTTATGTGATGAACCCAAAGGTCTCAAAACTGGAATGTGCATGgtatgtccatactccatagttccatgtcttgtttctatctgcacatcacgtgtacatgagtcacttgaagtaaaataccaaatatctcttatttcag------
|||||||||||  | || || |||||||||||||| || ||||| |||||||| |||||||||||||   | ||   ||   ||  ||||    ||   |  | |   |      | | ||| |    ||  ||     |  | | | || | |   ||       
GGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACTGGGATGTGCATGgtataagc-tatgtcac--ttgaatgttactttctgaattactttttttagatgcttgatttggctgctgtccctcattataaaactttgaaaacacaatgat

upper sequence: LOC_Os06g10280.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA12G08720.1 (Glycine max), 5'ss of exon 15
GGAAGGATGATACTTGCTCATTTATGTGATGAACCCAAAGGTCTCAAAACTGGAATGTGCATGgtatgt-ccatactccat-agttccatgtcttgtttctatctgcacatcacgtgtacatgagtcacttgaagtaaaataccaaatatctcttatttcag---
|| ||||||||  | || || |||||||||||||| || ||||| |||||||| |||||||||||||   |  |  | | | | ||  |  |  ||  | ||  |       | |  |   |  ||   |||      | ||  |||  | |   |   ||    
GGGAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACTGGGATGTGCATGgtataagctgtgttacttgaattttacattctgaat-tacttttttgagatgcttgatttggttg-ttgtccctcattataaaacctatgaaaacacaatga

upper sequence: LOC_Os06g10280.1 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv01s0010g00950.t01 (Vitis vinifera), 5'ss of exon 15
GGAAGGATGATACTTGCTCATTTATGTGATGAACCCAAAGGTCTCAAAACTGGAATGTGCATGgtatgtc-catact--ccatagttccat-gtcttgtttctatctgcacatcacgtgtacatgagtcacttgaagtaaaataccaaatatctcttatttcag
||||||||||| || || || || |||||||||||||| ||  | ||||||||||||||||||||||||   || ||  ||| |     || |  || | |    |||         | |       || ||         | ||       | |   || |  
GGAAGGATGATTCTGGCACACTTGTGTGATGAACCCAAGGGCTTGAAAACTGGAATGTGCATGgtatgttgtattctaaccagacaattattgagttatctgccactgtggtctctctcttttcccctccctctggcccccacacgcgccccccccctttccc-

upper sequence: LOC_Os06g10280.1 (Oryza sativa), 5'ss of exon 14
lower sequence: PP1S68_234V6.1 (Physcomitrella patens), 5'ss of exon 14
GGAAGGATGATACTTGCTCATTTATGTGATGAACCCAAAGGTCTCAAAACTGGAATGTGCATGgtatgtccatactccatagttccatgtcttgtttctatctgcacatcacgtgtacatgagtcacttgaagtaaaataccaaatatct-cttatttcag--------
||  || | || |||||||| || |||||||||||||| ||| | || ||||||||||||| |||| |||     ||  ||   | |  ||   |    |     ||||||||| |   | |  |  |    ||  | ||  | |||    || || |||         
GGTCGGCTAATTCTTGCTCACTTGTGTGATGAACCCAAGGGTTTGAAGACTGGAATGTGCACGgtacgtcgccgttct-taaacctaaatcgcat----agtccaacatcacgtatttgtcatgctgtctt-gttcactaggagatactggctaatatcaagagaaagc

upper sequence: LOC_Os06g10280.1 (Oryza sativa), 5'ss of exon 14
lower sequence: PP1S269_30V6.2 (Physcomitrella patens), 5'ss of exon 14
GGAAGGATGATACTTGCTCATTTATGTGATGAACCCAAAGGTCTCAAAACTGGAATGTGCATGgtatgtc-catactccatagttccatgtcttgtttctatctg-cacatcacgtgtacatgagtcacttgaag----taaaataccaaatatctcttatttcag
||  |  | || ||||| ||| |||||||||||||||||||| | || || |||||||||| |||| ||  ||   || | |  |  ||  | |  | | |   | ||   ||  ||||  | |||    | | |    | |  |     | |    ||| ||   
GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACAGGAATGTGCACGgtaagttgcagtttctaaacctgaattacctagtgcaaggcgtcattccagctgtagttcagttctctaatgggtgttagctgttttaaaatgattactt---

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|88265983|gb|CI376885.1|CI376885
EST:     GAACCCAAAGGTCTCAAAACTGGAATGTGCATG                         TCTCTGGTGTTTCTTCCTTTCCCTATTGCAAATGCTCTCACAGCAAAGATC
genomic: GAACCCAAAGGTCTCAAAACTGGAATGTGCATGgtatgtccat ... cttatttcagTCTCTGGTGTTTCTTCCTTTCGCTATTGCAAATGCTCTCACAGCAAAGATC
EST: gi|86435856|gb|CI107089.1|CI107089
EST:     TTGCTCATTTATGTGATGAACCCAAAGGTCTCAAAACTGGAATGTGCATG                         TCTCTGGTGTTTCTTCCTTTCGCTATTGCAAATGCTCTCACAGCAAAGATC
genomic: TTGCTCATTTATGTGATGAACCCAAAGGTCTCAAAACTGGAATGTGCATGgtatgtccat ... cttatttcagTCTCTGGTGTTTCTTCCTTTCGCTATTGCAAATGCTCTCACAGCAAAGATC
EST: gi|38483180|gb|CF966982.1|CF966982
EST:     TTGCTCATTTATGTGATGAACCCAAAGGTCTCAAAACTGGAATGTGCATG                         TCTCTGGTGTTTCTTCCTTTCGCTATTGCAAATGCTCTCACAGCAAAGATC
genomic: TTGCTCATTTATGTGATGAACCCAAAGGTCTCAAAACTGGAATGTGCATGgtatgtccat ... cttatttcagTCTCTGGTGTTTCTTCCTTTCGCTATTGCAAATGCTCTCACAGCAAAGATC

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: 48 (upstream exon), 75 (downstream exon)
Score: 18

GGAAGGATGATACTTGCTCATTTATGTGATGAACCCAAAGGTCTCAAAACTGGAATGTGCATGgtatgtccat ... cttatttcagTCTCTGGTGTTTCTTCCTTTCGCTATTGCAAATGCTCTCACAGCAAAGATCAATGCTGG




<











<


<