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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaagaggaaatatttttgaaggttttcgggccagcattcttgctcaaagttttgcaatcttattgtttcagGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATACTCATGAATGCAACTGACAAATCAAATAGAATGTTGCGGGCCAAATCGA

Basic information

species Oryza sativa
transcript LOC_Os03g49420.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49420.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 3
gtacaagaggaaatatttttgaaggttttcgggccagcattcttgctcaaagt---tttgcaatcttattgtttcagGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATACTCATGAATGCAACTGACAAATCAAATAGAATGTTGCGGGCCAAATCGA
||| |  ||||||||   || ||    |||  |  | |||  |     ||  |   ||| ||||||||||  |||||||||||||||||||||||||||||||||| |||||||| |||||| |||| ||||||||||||||||| ||||| || ||||||||||| |||||||| |
gtagatcaggaaatacagttcaat-ccttcttgttaacatagtaatctaacataaattttcaatcttatttattcagGAACACTTCCAAAAATATTATGATGCAGTAATGCCATACCTCAAGGCTATTCTCATGAATGCAACTGATAAATCCAACAGAATGTTGCGTGCCAAATCCA

upper sequence: LOC_Os03g49420.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G12120.1 (Glycine max), 3'ss of exon 4
gtacaagaggaaatatttt------tgaaggttttcgggccagcat-tcttgctcaaa-gttttgcaatcttattgtttc--agGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATACTCATGAATGCAACTGACAAATCAAATAGAATGTTGCGGGCCAAATCGA
|||      ||| |  |||      | ||  | | |     |   | | ||| |||    |||    ||  | || ||||  |||||||||||||||||||||||||||| || ||||||||||| ||  ||||| |  | |||||||| ||||| || ||  | ||| | || || || || |
gtattttgtgaacttctttgttcaatcaacatatgcaatttattttcttttgatcactcatttaattattatgttctttcttagGAACACTTCCAAAAATATTATGATGCTGTAATGCCATATCTGAAAGCTATATTGGTTAATGCAACCGACAAGTCTAACCGTATGCTTCGTGCTAAGTCCA

upper sequence: LOC_Os03g49420.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G28950.2 (Glycine max), 3'ss of exon 6
gtacaagaggaaatatttt------tgaaggttttcgggccagcat-tcttgctcaaa-gttttgcaatcttattgtttc--agGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATACTCATGAATGCAACTGACAAATCAAATAGAATGTTGCGGGCCAAATCGA
|||       || |  |||      | ||  |||       |   | | ||| |||    |||    ||  |  | ||||  |||||||||||||||||||||||||||| || |||||||| || ||| ||||| |  | ||||||||||||||||| ||  | ||| | || || || || |
gtattttgttaacttctttgttcaatcaacatttataatttattttcttttgatcactcatttaattattatggtctttcttagGAACACTTCCAAAAATATTATGATGCTGTAATGCCATACCTGAAGGCTATATTGGTTAATGCAACTGACAAATCTAACCGTATGCTTCGTGCTAAGTCCA

upper sequence: LOC_Os03g49420.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 4
------gtacaagag--gaaatatttttgaaggttttcgggccagca-ttcttgctcaaagttttgca-atcttattgtttcagGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATACTCATGAATGCAACTGACAAATCAAATAGAATGTTGCGGGCCAAATCGA
      ||| |  ||  |   |   | |   | ||| |   |  |||  ||||| || |||| |  || |   ||   ||  |||||||||| ||||| || |||||| | |||||||| ||||||||  ||||  | ||||||||||||||||| || ||  | ||| | || |||||||| |
gtatttgtaaagaagttgtgttgcatctattgttttccctacatgcaactcttgatctaagtctaacataatctaaatttgtagGAACACTTTCAAAAGTACTATGATACTGTCATGCCTTATCTCAAAACTATTTTGATGAATGCAACTGACAAGTCTAAGCGGATGCTTCGTGCCAAATCCA

upper sequence: LOC_Os03g49420.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 4
-------gtacaagaggaaatatttttg--aaggttttcgggccagcattcttgctcaaagttttgcaatcttattgtttcagGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATACTCATGAATGCAACTGACAAATCAAATAGAATGTTGCGGGCCAAATCGA
        ||    |  | ||  ||     | |||||||     |     |  ||  ||   |||  | | | | |     ||||||| ||||||||||| ||||||||||| ||||| || || ||  | ||| | |||||||| |||||||| || ||  | ||| | || |||||| | |
gtattatatattttaaaatatgcttccattatggttttcttataaatgagca-gcctaacacttttgagtatcaat-----agGAACATTTCCAAAAATACTATGATGCAGTTATGCCTTACCTAAAAGCAATATTGATGAATGCCACTGACAAGTCTAACCGCATGCTTCGTGCCAAAGCCA

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|29679231|gb|CB675506.1|CB675506
EST:     TGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAC                         GAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATA
genomic: TGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtacaagagg ... attgtttcagGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATA
EST: gi|571970|gb|D41481.1|D41481
EST:     TGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAG                         GA-CACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATA
genomic: TGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtacaagagg ... attgtttcagGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATA
EST: gi|569698|gb|D40547.1|D40547
EST:     TGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAG                         GAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATA
genomic: TGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtacaagagg ... attgtttcagGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATA
EST: gi|29629840|gb|CB634849.1|CB634849
EST:     TGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAG                         GAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATA
genomic: TGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtacaagagg ... attgtttcagGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaggttttcgggccagcattcttgctcaaagttttgcaatcttattgtttcagGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATACTCATGAATGCAACTGACAAATCAAATAGAATGTTGCGGGCCAAATCGA
                                         tcttatt  CT-rich tract
                                       aatcttatt  TA-rich tract