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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTGCAGAGGAAGACTGAAGAAGCTGCGATGGCTACCAAAAGGCTGAAAGAGTTACTAGAGGCTCGGAAATCATCAGGACGTGACAACTCAGgtatctctctccgcattgcgaccatttttcgcattataattaatactcccaatctaacagctcttccttctttttctttttttttttttttgctttcttccaaacacatcag

Basic information

species Oryza sativa
transcript LOC_Os09g02650.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g02650.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G026218_T02 (Zea mays), 5'ss of exon 18
GTTTTGCAGAGGAAGACTGAAGAAGCTGCGATGGCTACCAAAAGGCTGAAAGAGTTACTAGAGGCTCGGAAATCATCAGGACGTGACAACTCAGgtatctctctccgcattgcgaccattt---ttcgcat-tataattaatactcccaatctaacagctcttccttctttttctttttttttttttttgctttcttccaaacacatcag-----------------------------------------------------
|||||||| |||||||| ||||| ||||| |||||||| ||||||||||||||| || |||| ||| ||||||| || |  |||||||  || ||||||| |||| ||||   |||  | |   || |  |  |  |  ||||||   |||||||  | ||  || | || |||  | |     |   ||    |      |||  |||                                                      
GTTTTGCAAAGGAAGACCGAAGAGGCTGCTATGGCTACAAAAAGGCTGAAAGAGATATTAGAAGCTAGGAAATCTTCCGCCCGTGACAGTTCCGgtatctttctctgcatcttgacattatgtatttgtgtacactaaaaatactttgaatctaatggttc--ccctgttcttccctctaaacatagctggcagcaatggtacatctcaaggctataatgtaagattatctatacctaacattcctaagtttatttacacaat

upper sequence: LOC_Os09g02650.1 (Oryza sativa), 5'ss of exon 18
lower sequence: AT5G47820.1 (Arabidopsis thaliana), 5'ss of exon 16
GTTTTGCAGAGGAAGACTGAAGAAGCTGCGATGGCTACCAAAAGGCTGAAAGAGTTACTAGAGGCTCGGAAATCATCAGGACGTGACAACTCAGgtatctctctccgcattgcgaccatttttcgcattataattaatactcccaatctaacagctcttccttctttttctttttttttttttttgctttcttccaaacacatcag--
||| | ||||||||||| ||||| ||||| ||||||||||||||| ||||||||||  |||| ||||| ||||||||    |||||  ||||||||||        | ||  | |   |||     | |  ||| | |    |  |      ||||  |  || |  ||| ||||  |  | |        || ||   | |  ||  
GTTCTTCAGAGGAAGACAGAAGAGGCTGCAATGGCTACCAAAAGGTTGAAAGAGTTGTTAGAAGCTCGAAAATCATCTCCTCGTGAACACTCAGgtat--------gaataacaatacttt-----aatggaatca-tgtcactgagtatttagctgattgttgtgattcattttcatagtctactggaaattgcacgtaaagtagtt

upper sequence: LOC_Os09g02650.1 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv18s0001g10090.t01 (Vitis vinifera), 5'ss of exon 18
GTTTTGCAGAGGAAGACTGAAGAAGCTGCGATGGCTACCAAAAGGCTGAAAGAGTTACTAGAGGCTCGGAAATCATCAGGACGTGACAACTCAGgtat---ctctctccgcattgcg-accatttttcgcattataattaatactcccaatctaacagctcttccttctttttctttttttttttttttgctttcttccaaacacatcag
||| | ||| | ||||| || |||||||| ||||| ||||||||||| |||||||| ||||| ||||| || || |||| |||||| |||||||||||    | |||  | |||      | ||| | |  |  | |||   ||||  || | |  ||  |  |||  ||||  |   |     ||                        
GTTCTTCAGCGAAAGACAGAGGAAGCTGCTATGGCCACCAAAAGGCTAAAAGAGTTGCTAGAAGCTCGCAAGTCTTCAGCACGTGAAAACTCAGgtatgttttttctttgaattttatgtcttttataggctggtgatttggactcttaaccaagaagtacaccctcattttaataaataaagcttcagaaagg----------------

upper sequence: LOC_Os09g02650.1 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv07s0031g00130.t01 (Vitis vinifera), 5'ss of exon 18
GTTTTGCAGAGGAAGACTGAAGAAGCTGCGATGGCTACCAAAAGGCTGAAAGAGTTACTAGAGGCTCGGAAATCATCAGGACGTGACAACTCAGgtatctctctccgcattgcgaccatttttcgcattataattaatactcccaatctaacagctcttccttctttttctttttttttttttttgctttcttccaaacacatcag
||| | || || || || ||||| |||||  | ||||||||||||||||||||||||||||| ||||| ||||| |||| |||||| || || ||||  |   |      |      | ||||| ||| ||  |  || ||     |||||    | | | |||| ||||                                    
GTTCTTCAAAGAAAAACAGAAGAGGCTGCAGTAGCTACCAAAAGGCTGAAAGAGTTACTAGAAGCTCGCAAATCTTCAGCACGTGATAATTCCGgtacataaatgttttctcttgaaaattttc-catcatcctatattcttattttctaatca-tgtgctttctatttcag----------------------------------

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|58657321|gb|CK046001.1|CK046001
EST:     TCGGAAATCATCAGGACGTGACAACTCAG                         GCATGAATGGTACTTCTCCTGGCTCTCAT
genomic: TCGGAAATCATCAGGACGTGACAACTCAGgtatctctct ... aacacatcagGCATGAATGGTACTTCTCCTGGCTCTCAT
EST: gi|58661888|gb|CK050568.1|CK050568
EST:     GCTGAAAGAGTTACTAGAGGCTCGGAAATCATCAGGACGTGACAACTCAG                         GCATGAATGGTACTTCTCCTGGCTCTCAT
genomic: GCTGAAAGAGTTACTAGAGGCTCGGAAATCATCAGGACGTGACAACTCAGgtatctctct ... aacacatcagGCATGAATGGTACTTCTCCTGGCTCTCAT
EST: gi|58682531|gb|CK071218.1|CK071218
EST:     GCTGAAAGAGTTACTAGAGGCTCGGAAATCATCAGGACGTGACAACTCAG                         GCATGAATGGTACTTCTCCTGGCTCTCAT
genomic: GCTGAAAGAGTTACTAGAGGCTCGGAAATCATCAGGACGTGACAACTCAGgtatctctct ... aacacatcagGCATGAATGGTACTTCTCCTGGCTCTCAT

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: 67 (upstream exon), 29 (downstream exon)
Score: 21

GTTTTGCAGAGGAAGACTGAAGAAGCTGCGATGGCTACCAAAAGGCTGAAAGAGTTACTAGAGGCTCGGAAATCATCAGGACGTGACAACTCAGgtatctctct ... aacacatcagGCATGAATGGTACTTCTCCTGGCTCTCAT




<











<


<