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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgcatagaaacagacatgttttgggtgcatacatgttctgcaagtgtcttttcttggctt...

Basic information

species Oryza sativa
transcript LOC_Os01g23610.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G145595_T02 (Zea mays), 5'ss of exon 4
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaa-cacatgcatagaaa---cagacatgtt--ttgggtgcatacatgttctgcaagtgtcttttcttggctt
||||||||||||||||||||| ||||| ||||||||||| || ||||| |||||||||||||| |||||||||||||||||||| ||||| |||||||||||| ||||||| |   | |    |||||||   |||  |||||| |||  |    |  | ||||  ||   |      || |||  |     | | |  |      
TGCACTAAAACTTGAGTCAGTCCCTGAATGGATTGCTATTGTTGGAAGTGGTTACATTGGACTTGAATTCAGTGATGTATACACAGCTCTAGGAAGTGAGgtatatgaacaatcattcaagc-catcattgcttaaatacatgcttagggagtctaatcgtgttagttattttagcgaatattcctctgtcatatatcatg-----

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA15G15310.1 (Glycine max), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgc--atagaaacagacatgttttgggtgcatacat--gttctgcaagtgtcttttcttggctt-------------------------------------------------------------------------------------------
|||||| ||||| ||| | |||||||| ||||| || || || ||||| ||||| ||||| || ||||||||||||||||| ||||| || ||||||||||||   | ||   || |  |||  ||  |||| || |   |    || | |         |     |  |  |||   ||| | ||| | |  |||  || | |                                                                                           
TGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGATGTATATACGGCCCTTGGAAGTGAGgta---gtacttctcttctgatatatttttttttatcctttctcaattgtattttgttcatgagaagaactgacaatagttttccaatttttcttttatgacgtttgaaagttttttatattatctcattgtttgaaaagttagaaacctaatttgtgcagaagagatatagttggtaataatggtactctgcag

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA07G37050.2 (Glycine max), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgcatagaaacagacatgttttgggtgcatacatgttctgcaagtgtcttttcttggctt-
 ||||| ||||| || || |||||||| ||||| || || || ||||| || || ||||| || ||||||||||||||||| || || || ||||||||||||     |   ||   ||  |  ||  ||||        |    |  | |     |  ||  |    ||  |         | |    |   ||| | | 
CGCACTCAAACTGGAATCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGATGTATATACAGCACTTGGAAGTGAGgta-gcacatctttgtgaattttgatactttttctttctcttttcattaccttttgttcttgagaaatatttacaaataatcaatcctatcatttgacatc

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgcatagaaacagacatgttttgggtgcatacatgttctgcaagtgtcttttcttggctt--------
 ||||| ||||| ||||| |||||||| ||||| || || || ||||| || || ||||| || ||||||||||||||||| || || || ||||||||||||   | ||| |   |  |||  |   |||  |      | |||   | |     |  ||       ||  ||          |  |||   ||| | |        
CGCACTCAAACTGGAGTCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGATGTATATACAGCACTTGGAAGTGAGgta---gcaca-tctttgtgat--actgtttctttcttttttcatt--accttttgttcttgataaatatttataaataatcgatcccttcatttgacatcagaaata

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgta-catgaacagttcctaagatgcatcattttctaacacatgcatagaaacagacatgttttgggtgcatacatgttctgcaagtgtcttttcttggctt--
|||  | ||| | ||||| || ||||| |||||||| || || ||||| ||||| ||||| || || ||||||||||| ||||| ||||| |||||||||||| |||||    |   ||  |   ||  |  | ||  ||   | | |  |  |   |||  | | | | |     |     || ||   ||       ||  
TGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgtaacatgatgtttctgtactaatgatattactttagtacg-actttgtgat-gttgtgtccttg-tacttgagattgtaataactgcaattagcaatgttct

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgcatagaaaca-gacatgttttgggtgcatacatgttctgcaagtgtcttttcttggctt------
|||| | ||| | ||||| ||||||||||||||||| || || ||||| ||||| || || || || ||||||||||| |||||||| || ||||||||||||     ||| ||   |   ||    | |   |  |||  |  |   |    |   | ||||| || | |   |  | | |   | ||| |   | |         
TGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGATGTTTACACGGCCCTTGGAAGTGAGgta-----aca-ttttgattttgtgctaatgatttgcactggtgtgatagtgtgttgttttttgcgttc-tctttagttttctgttttctctcaatagtaacaaaag

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgcatagaaacagacatgttttgggtgcatacatgtt-ctgcaagtgtcttttcttggctt-
||| || ||||| ||||| |||||||| ||||| || || || ||||| ||||| ||||| || |||||||||||||| || || || || ||||||||||||         ||  ||         |||       | ||  ||| |||  || |  |||             ||| | ||     |||  |  |    | 
TGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAGgta-gcatcttctttatagtcattgcgattacagtttaaatttatataaat-gagaaatttcaatcaatagtgagttacagcttagatctggtgctaaaatc

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgcatagaaacagacatgttttgggtgcatacatgt-tctgcaagtgtcttttcttggctt---------------------
||| || || || ||||   | || ||||||||||| || || ||||| ||||||||||| || || ||||| ||||| || || || || |||||||||||| |     | |||||     |||| |||     |||     ||| ||   ||  |||   | | |  |  |  | ||||  | |   |     || |||                     
TGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGATGTCTATACTGCCCTTGGAAGTGAGgtaaa-----atttccttg--cgcattatt----gacaataaaataaaagtggatgtgtggagtgcgtgtgtaattatctgacaataattggagctgacttcccttttctgtgggcttgcag

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagtt--cctaagat------gcatcatt-ttctaacacatgcatagaaacagac--atgttttgggtgcatacatgttct-gcaagt-gtcttttcttggctt-------
 ||  | ||  | ||||   |||| ||||||||||| ||||| || |||||||||||||| || || ||||||||||||||||| ||||| ||||| |||||   | | |  ||  |  | | |      ||||  || || ||    ||   |  |    | |  || | ||     | |  |||  ||  ||||| | | | | || |          
CGCTTTGAAGTTAGAGTGGATTCCAGACTGGATTGCGATCGTTGGCAGCGGTTACATTGGTCTAGAGTTCAGTGATGTATACACAGCTCTCGGAAGCGAGgtcagtaaccgtttgtctcacggtctaggagcatttttattttattctattttttcactttgtcgtatatcttcatcacttgtatggactcacaagttgacctcttttcgtgcccggcag

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgcatagaaacagacatgttttgggtgcataca--tgt--tctgcaagtgtcttttcttggctt---------------
|||  | || || ||||   |||| ||||||||  |||| || ||||| ||||||||||| || || ||||||||||| ||||| || || ||||| |||||||| |     ||   | ||  ||  |||||  || | |   || || | |     ||| | | |  | | |  |||  |||    | |  | || |   |||               
TGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGATGTTTACACTGCCCTTGGAAGCGAGgtaca-gttttattgaaaggacacaatatttttaaaaata-aaatggatatat-tgggttctagttttaaaaagttgtcatctagtggagcttattttcctcttgctgtgggttggcag

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|58684178|gb|CK072865.1|CK072865
EST:     GTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAG                         GTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCT
genomic: GTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaac ... acttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCT