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'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   		34  
 5'  3'   		35  
 5'  3'   		36  
 5'  3'   		37  
 5'  3'   		38  
 5'  3'   		39  
 5'  3'   		40  
 5'  3'   
41  
 5'  3'   		42  
 5'  3'   		43  
 5'  3'   		44  
 5'  3'   		45  
 5'  3'   		46  
 5'  3'   		47  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGTCATTCCCCCCAGCTGCATTCAAATGCGCAATGTTATTCTTAGTGCTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAGgtatttactggttgtgtttatgtaacacttactctaatgcttttccacgctattgtatgtttgatcaacttaaccatttttttgcaacacag

Basic information

species Oryza sativa
transcript LOC_Os10g40780.3
intron # 43
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g40780.1 (Oryza sativa), 5'ss of exon 46
lower sequence: PP1S85_31V6.1 (Physcomitrella patens), 5'ss of exon 46
TGATGTCATTCCCCCCAGCTGCATTCAAATGCGCAATGTTATTCTTAGTGCTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAGgtatt-tactggttgtgtttatgtaacacttactctaatgcttttccacgctattgtatgtttgatcaacttaaccatttttttgcaacacag-------------------------------------------------------
|||||| ||||||||   ||| ||||| ||||||||| | |||||||| |||||||||||||| ||| ||||||| ||||| | ||| || ||||| ||||||   || |  |  | |  |  |   |  |   |  ||    |  ||   |  |  || ||| |  || | ||   ||  ||||   |                                                           
TGATGTGATTCCCCCATCCTGTATTCAGATGCGCAATCTAATTCTTAGCGCTTTTCCACGCAACATGCGACTTCCTGATCCTTTTACACCTAATTTGAAGgtagcatattcatattttcaaccttcaaactttgcagatagcctatcaattttgttcatttttaaa-aagtaaatatttcctttgtggctgttatatgtaaattggaaggcacaaaagtcagctatctaaggcgtggtgtttaatcag

upper sequence: LOC_Os10g40780.1 (Oryza sativa), 5'ss of exon 46
lower sequence: EFJ17138 (Selaginella moellendorffii), 5'ss of exon 35
TGATGTCATTCCCCCCAGCTGCATTCAAATGCGCAATGTTATTCTTAGTGCTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAGgtatttactggttgtgtttatgtaacacttactctaatgcttttccacgctattgtatgtttgatcaacttaaccatttttttgcaacacag
 || ||||||||||| ||||| ||||||||||| ||| | || || || || || ||||| |||||| |||| |||||||| | ||||||||| || ||||||||   ||  | ||||  ||      ||     |||| | ||   |||                                          
CGACGTCATTCCCCCGAGCTGTATTCAAATGCGTAATCTCATACTGAGCGCATTCCCACGAAATATGCGACTGCCAGATCCATTTACTCCAAACTTGAAGgtattccgtgcat-tgttgttgacgtctttgtgacaatggtattt-gcgcag----------------------------------------
















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|12405034|gb|AU166635.1|AU166635
EST:     CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAG                         ATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT
genomic: CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAGgtatttactg ... tgcaacacagATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT
EST: gi|428676|gb|D24828.1|D24828
EST:     CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAG                         ATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT
genomic: CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAGgtatttactg ... tgcaacacagATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT
EST: gi|58681156|gb|CK069843.1|CK069843
EST:     CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAG                         ATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT
genomic: CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAGgtatttactg ... tgcaacacagATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT
EST: gi|428473|gb|D24623.1|D24623
EST:     CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAG                         ATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT
genomic: CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAGgtatttactg ... tgcaacacagATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT
EST: gi|33679180|gb|CF307419.1|CF307419
EST:     CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAG                         ATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT
genomic: CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAGgtatttactg ... tgcaacacagATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT
EST: gi|163928760|gb|EG711897.1|EG711897
EST:     CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAG                         ATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT
genomic: CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAGgtatttactg ... tgcaacacagATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT
EST: gi|428499|gb|D24650.1|D24650
EST:     CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAG                         ATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCANGTCTGATGTT
genomic: CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAGgtatttactg ... tgcaacacagATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT
EST: gi|58677103|gb|CK065790.1|CK065790
EST:     CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAG                         ATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT
genomic: CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAGgtatttactg ... tgcaacacagATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT
EST: gi|428675|gb|D24827.1|D24827
EST:     CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAG                         ATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT
genomic: CTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAGgtatttactg ... tgcaacacagATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTT

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: 72 (upstream exon), 60 (downstream exon)
Score: 20

TGATGTCATTCCCCCCAGCTGCATTCAAATGCGCAATGTTATTCTTAGTGCTTTTCCACGCAATATGAGACTTCCAGATCCCTCTACTCCAAATTTAAAGgtatttactg ... tgcaacacagATTGATCTTCTTGCTGAGATTTCAATTCCTCCAAGAATCATGTCTGATGTTGATGGTGCCTTAAAGTCAAAGCAAATGAAGACACAGGTTGATGAGTACC




<











<


<