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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTTGCTCCAATGCCTACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAATGCTTTGAACCTTATACATCTAACATATACAGCCGGCGGGTTCTAAGgtttgtaactacactgttcttagtgctcgtgctcactacaggtgcttatgattgattttgtttaattcttttccag

Basic information

species Oryza sativa
transcript LOC_Os06g07210.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07210.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G340527_T01 (Zea mays), 5'ss of exon 13
TTGTTGCTCCAATGCCTACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAATGCTTTGAACCTTATACATCTAACATATACAGCCGGCGGGTTCTAAGgtttgtaactacactgtt--ctt------agtgctcgtgctca---ctacaggtgcttat--gattgattttgtttaattcttttccag
|||||||||||||||| ||||||||||||||||||||||||||||||||||| ||||||||||| || |||||||| || ||||| || ||||||||||||| |||||| | ||| ||  |||      |||| |     |      |||| |||| |||  ||||||| || | || || | ||||||
TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaacaatactctttacttctttagagtgtttacattttgacttacatgtgcatatatgattgatctt-tctatttttattccag

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G304362_T01 (Zea mays), 5'ss of exon 13
TTGTTGCTCCAATGCCTACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAATGCTTTGAACCTTATACATCTAACATATACAGCCGGCGGGTTCTAAGgtttgtaactacactg------ttcttagtgc-------tcgtgctcactacaggtgcttatgattgattttgtttaattcttttccag
|||||||||||||||| ||||||||||||||||||||||||||||||||||| || |||||||| || || ||||| |||||||| || || |||||||||| |||||| | |||       |  |||| |        | ||| |    |   |  | | ||||| || ||  |   || | ||||||
TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGTTTTGAACCCTACACGTCTAATATATACAGTCGACGTGTTCTAAGgtctgtaacaatactccctacttctttagggtgtttacattgtgatgtacatgtgcacatgtgattaatctttctattttttgttccag

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA06G15350.1 (Glycine max), 5'ss of exon 13
TTGTTGCTCCAATGCCTACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAATGCTTTGAACCTTATACATCTAACATATACAGCCGGCGGGTTCTAAGgtttgtaactaca--ctgttcttagtgctcgtgctcactacag----gtgcttatgattgattttgtt-taattcttttccag
| || || || ||||||||||| || ||||| ||||||||||| || || || || |||||||| ||||| || ||||||||||| ||  | ||| |||||||||    | ||  |  || ||  ||     |   ||||  |     || |  |   | | |  | |    ||  |||| ||
TCGTGGCCCCTATGCCTACTGCATCTACTAGCCAGATTCTTGGAAATAACGAGTGTTTTGAACCATATACTTCAAACATATACAGTCGTAGAGTTTTAAGgtttgctttttcatcccattttttctgtcttggtgtactattgcctcatgatcctatcttactgggctactgtttgtttctag

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA04G39500.1 (Glycine max), 5'ss of exon 13
TTGTTGCTCCAATGCCTACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAATGCTTTGAACCTTATACATCTAACATATACAGCCGGCGGGTTCTAAGgtttgtaactacactgttcttagtgctcgtgctcactacaggtgcttatgattg-attttgtttaa------ttcttttccag
| || || || ||||| ||||| |||||||| ||||||||||| || ||||| || |||||||| ||||| || || || ||||| ||  | ||| |||||||||    | | |   | ||| |     |         |  | |  |||||   || || ||         ||  |||| ||
TCGTGGCCCCTATGCCAACTGCATCCACTAGCCAGATTCTTGGAAATAATGAGTGTTTTGAACCATATACTTCAAATATCTACAGTCGTAGAGTTTTAAGgtttgctttttcgcccgtgttattctgtcttggtgtattattttcccatgatcctatcttattgggcaactgtttgtttctag

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA08G15360.1 (Glycine max), 5'ss of exon 15
--------TTGTTGCTCCAATGCCTACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAATGCTTTGAACCTTATACATCTAACATATACAGCCGGCGGGTTCTAAGgtttgtaactacactgttcttagtgctcgtgctcactacaggtgcttatgattgattttgtttaattcttttccag-------------------------
        ||||||| || ||||| ||||| || ||||| |||||||||||||| ||||| || ||||| || ||||| ||||| || ||||| ||  | ||| ||||| |  |  |   ||  | |||| |  |  |    |    |      |||  |   | ||   |  || | || |||                         
CTCACTTCTTGTTGCCCCTATGCCAACTGCATCAACTAGCCAGATTCTTGGCAATAATGAGTGTTTTGAGCCATATACTTCTAATATCTACAGTCGTAGAgttttaaggctcattgccgtaccat-cttattattttttgatatcttattgatctattttgattgttaactgtttgtctttcagtggtgaatttgttgtggtgaacaag

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA05G32070.1 (Glycine max), 5'ss of exon 13
TTGTTGCTCCAATGCCTACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAATGCTTTGAACCTTATACATCTAACATATACAGCCGGCGGGTTCTAAGgtttgtaactacactgttcttagtgctcgtgctcactacaggtgcttatgattgattttgtttaattcttttccag
||||||| || ||||| ||||| || ||||| |||||||||||||| ||||| || ||||| || ||||| ||||| || ||||||||  | |||||||||||| |  | | |   | |||| |     |    |    |      |||  |   | ||   |  || | || |||
TTGTTGCCCCTATGCCAACTGCATCAACTAGCCAGATTCTTGGCAATAATGAGTGTTTTGAGCCATATACTTCTAATATCTACAGCCGCAGAGTTCTAAGgtttattgccatatcat-cttattatgttttgatatcttattgatctatcttgattgttaactgtttgtctttcag

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT2G21790.1 (Arabidopsis thaliana), 5'ss of exon 13
TTGTTGCTCCAATGCCTACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAATGCTTTGAACCTTATACATCTAACATATACAGCCGGCGGGTTCTAAGgtttgtaactacactgttctt-----agtgc---tcgtgctcactacaggtgcttatgattgattttgtttaattcttttccag--
| || || |||||||| |||||||| || ||||| || ||||| ||||||||||| ||||| || || ||||| ||||| ||||||||  | ||  | |||| ||| | ||     |  ||     |||     ||  | |  |  ||  || |  | | | | || |||   ||  |||  |   
TAGTAGCACCAATGCCAACTGCTTCAACCAGTCAAATCCTTGGGAACAATGAATGTTTTGAGCCCTACACATCAAACATCTACAGCCGCAGAGTCTTGAGgtatgtgaatattaaatcatttgacaagtatgtttctggttttccccatttgatgcttactcacttggttgtcttggtttgtacag

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 5'ss of exon 13
TTGTTGCTCCAATGCCTACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAATGCTTTGAACCTTATACATCTAACATATACAGCCGGCGGGTTCTAAGgtttgtaactacactgttcttagtgctcgtgctcactacaggtgcttatgat-tgattttgtttaattcttttccag------------
|||| || || ||||| |||||||| || || ||||||||||| |||||||| |||||||| || ||||| || || || |||||  || | ||||||||||||||      ||  |     || |   | || |      || ||| || |   || |   |    ||||| |  |            
TTGTAGCACCTATGCCCACTGCTTCAACCAGCCAGATTCTTGGAAACAATGAGTGCTTTGAGCCCTATACTTCCAATATCTACAGTAGGAGAGTTCTAAGgtttgttttgctaccctaacctgttcattttctaagatttagtacttttgttgccatctaagtctcctctttccttgtttctttgtcag

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 5'ss of exon 13
lower sequence: EFJ14283 (Selaginella moellendorffii), 5'ss of exon 12
TTGTTGCTCCAATGCCTACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAATGCTTTGAACCTTATACATCTAACATATACAGCCGGCGGGTTCTAAGgtttgtaactacactgttcttagtgctcgtgctcactacaggtgcttatgattgattttgtttaattcttttccag
|||||||||||||||| || || || || || || |||||||| ||||| || || ||||| ||||||||||| || || ||||  || || |||||||||| ||        ||||  | ||   |  | || |     | ||| |   |  |                      
TTGTTGCTCCAATGCCGACAGCATCAACAAGCCAAATTCTTGGAAACAACGAGTGTTTTGAGCCTTATACATCCAATATTTACACTCGACGCGTTCTAAGgtatgccttctttctgta-tcagctgtgatacttat----gttgcctgccacag----------------------

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 5'ss of exon 13
lower sequence: EFJ20162 (Selaginella moellendorffii), 5'ss of exon 1
TTGTTGCTCCAATGCCTACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAATGCTTTGAACCTTATACATCTAACATATACAGCCGGCGGGTTCTAAGgtttgtaactacactgttcttagtgctcgtgctcactacaggtgcttatgattgattttgtttaattcttttccag
|||||||||||||||| || || || || || || |||||||| ||||| || || ||||| ||||||||||| || || |||   || || |||||||||| ||        ||||  | ||   |  | || |     | ||| |   |  |                      
TTGTTGCTCCAATGCCGACGGCATCAACAAGCCAAATTCTTGGAAACAACGAGTGTTTTGAGCCTTATACATCCAATATTTACGCTCGACGCGTTCTAAGgtatgccttctttctgta-tcagctgtgatacttat----gttgcctgctacag----------------------

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 5'ss of exon 13
lower sequence: EFJ20157 (Selaginella moellendorffii), 5'ss of exon 12
TTGTTGCTCCAATGCCTACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAATGCTTTGAACCTTATACATCTAACATATACAGCCGGCGGGTTCTAAGgtttgtaactacactgttcttagtgctcgtgctcactacaggtgcttatgattgattttgtttaattcttttccag
|||||||||||||||| || || || || || || |||||||| ||||| || || ||||| ||||||||||| || || ||||  || || |||||||||| ||        ||||  | ||   |  | || |     | ||| |   |  |                      
TTGTTGCTCCAATGCCGACAGCATCAACAAGCCAAATTCTTGGAAACAACGAGTGTTTTGAGCCTTATACATCCAATATTTACACTCGACGCGTTCTAAGgtatgccttctttctgta-tcagctgtgatacttat----gttgcctgctacag----------------------

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|88274010|gb|CI394416.1|CI394416
EST:     GAATGCTTTGAACCTTATACATCTAACATATACAGCCGGCGGGTTCTAAG                         TGGGGAGTTTGTTGTGGTTAACAAGCATCTTCTCCATGATTTG
genomic: GAATGCTTTGAACCTTATACATCTAACATATACAGCCGGCGGGTTCTAAGgtttgtaact ... tcttttccagTGGGGAGTTTGTTGTGGTTAACAAGCATCTTCTCCATGATTTG




















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: 74 (upstream exon), 70 (downstream exon)
Score: 12

TTGTTGCTCCAATGCCTACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAATGCTTTGAACCTTATACATCTAACATATACAGCCGGCGGGTTCTAAGgtttgtaact ... tcttttccagTGGGGAGTTTGTTGTGGTTAACAAGCATCTTCTCCATGATTTGACTGAAATGGGTGTTTGGACTCCAGCTCTGAAAAATAAGATAATTTATGAAGATGGT




<











<


<