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

...taaggaccttttattaatgaatttggcaaagaattgcacatcatattctgttggcatttatcaatattgtatcttctggtttgaatgatccaatatgcagGAGAAGAAAACTATTCGCCCTACATTTTCAGCTGAACGTATTTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGG

Basic information

species Oryza sativa
transcript LOC_Os06g05180.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 12
-----taaggaccttttattaatgaatttggcaaagaattgcacatcatattctgttggcatttatcaatattgtatcttctggtttgaatgatccaatatgc-agGAGAAGAAAACTATTCGCCCTACATTTTCAGCTGAACGTATTTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGG
       |   |||||| || |    |||  |||||||  ||||||   | ||| |||||||||      |||||||  | ||  || ||| |||  || |   |||||||||||||||| |||||| |||||||||| || ||||||| ||||||  |||| ||||| |||||||| ||||| ||||| ||||||||||||||||
ttgtgacatagcctttttttgaattgtttcacaaagaa--gcacattgcaatcttttggcattttc----attgtattctgtgacttaaattatctgattttttagGAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTATGGTGGGGTATTGTTGGCAATGTGTTCTAGTGACTTCATCTGCTTTTATGACTGGG

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G095348_T03 (Zea mays), 3'ss of exon 12
-------taaggaccttttattaatga-atttggcaaagaattgcacatcatattctgttggcatttatcaatattgtatcttctggtttgaatgatccaatatg-cagGAGAAGAAAACTATTCGCCCTACATTTTCAGCTGAACGTATTTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGG
       | | |    |    ||   | ||||  |||| |   ||||||  || ||| |||| |||  |||      | || | ||  || ||| |||  || |  ||||||||||||||||| |||||| |||||||||| || ||||||||||||||  |||| ||||| |||||||| ||||||||||| ||||||||||||||||
gcaaatgtgaagtttctgatctagccatatttcacaaaaa---gcacattctaatcttttggtattc-tca-----ttgtcctgtgacttaaattatctgatttttcagGAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGG

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 12
taaggaccttttattaatg-aatttggcaaagaattgcacatcatattctgttggcatttatcaatattgtatcttctgg---tttgaatgatccaatatgcagGAGAAGAAAACTATTCGCCCTACATTTTCAGCTGAACGTATTTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGG
      ||| | |||  |  |   |   |      | |  ||   | |   || ||  |    |||| |   | |  | |   ||| ||  ||      | ||||| ||||  | | | || || ||||||||||||||| | || |||||||| |   || |||||||||| ||||  |||||||| ||||||||||||||||
----atcctctcattgttataggcttatagctgtcttcgtattgaaataaatttgctctagggaatacttggtttagttggaatttaaacaattggtatttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAAAGAATATTTGGTGGCACTCTACTGGCGATGTGCTCCAACGATTTCATCTGCTTTTATGACTGGG

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 12
----taaggaccttttattaatgaatttggcaaagaattgcacatcatattctgttggcatttatcaatattgtatcttctggtttgaatgatccaatatgcagGAGAAGAAAACTATTCGCCCTACATTTTCAGCTGAACGTATTTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGG
    |     ||| | |||  |  |  || |   |||||| |    || | || | || | |  | | | | ||    |    ||| ||  ||      | ||||| ||||  | | | || || ||||||||||||||| | || || ||||| |  ||| |||||||||| ||||  |||||||| ||||||||||||||||
aaaatttaatcctatcattgttatagctgtcttcgaattgaaataaatttgctctagggaatacttagtttagt----tggaatttaaacaatgggtatttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAAAGAATATTCGGTGGCACTTTACTGGCGATGTGCTCCAACGATTTCATCTGCTTTTATGACTGGG

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 1
----taaggaccttttattaatgaatttggcaaagaattgcacatcatattctgttggcatttatcaatattgtatcttctggtttgaatgatccaatatgcagGAGAAGAAAACTATTCGCCCTACATTTTCAGCTGAACGTATTTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGG
     ||  || || | ||| ||  || |   | |  || || || |  |     | |  | ||   |  || ||  ||     |  |||  |  |   | ||||| ||||| | ||| || || || |||||||||||||| || |||||||| |   ||||||| ||||| || | ||||||||| ||||||||||| ||||
caaaaaataacattctcttattgttttag---atgtcttccaaatgaactataagttgtctctagggaagttttaa-ttggaaatgaaattttgtatatttcagGAAAAGAAGAGTATCCGACCAACTTTTTCAGCTGAACGAATATTTGGTGGCACTGTATTGGCAATGTGCTCAAATGATTTCATCTGCTTTTATGATTGGG

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 12
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 12
-------------------------taaggaccttttattaatgaatttggcaaagaattgcacatcatatt-ctgttggcatttatcaatattg-tatcttctggtttgaatgatcca--------atatgcagGAGAAGAAAACTATTCGCCCTACATTTTCAGCTGAACGTATTTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGG
                           | | | || | || |    | |  | | |  |||       ||||  || |     | ||  | || | ||| ||| | | ||  | || ||        || | ||||| ||||  | ||| |||||||| |||||||||||    || ||||| ||||  || || || |||||||| ||||||||||| ||||||||||| ||||
gtttctaaatctttttctctctgatctaagccgttctgttcaaccctgtatctatgg-ttgttggaagtattattgatactggtcatggagatagctatattcggatctggctcattcagaaaatacattttcagGAAAAGAGGAGTATCCGCCCTACTTTTTCAGCTGAGAAGATCTTTGGAGGAACCTTGTTAGCTATGTGTTCAAGTGATTTCATCTGCTTTTATGATTGGG

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 12
taaggaccttttattaatgaatttggcaaagaattgcacatcatattctgttggcatttatcaatattgtatcttctggtttgaatgatccaatatg---cagGAGAAGAAAACTATTCGCCCTACATTTTCAGCTGAACGTATTTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGG
  |   |||   | |  ||  | |||  |  | |   |  | |       |       | |    |     ||  | |  || |||||      ||    ||||| ||||  | | | || || |||||||||||||| | ||||||||| ||||  |||||||| ||||| || | |||||| ||||| || ||||||||||
-tattgcctgccactgttg--tctggttacaagtgttaggtaaatgcaaatatattcctgttcggagaaattcaacagagtttaatgaagtggcatctttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGG

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|29630380|gb|CB635389.1|CB635389
EST:     CTATCAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAG                         GAGAAGAAAACTATTCGCCCTACATTTTCAGCTGAACGTATTTTTGGTGGA
genomic: CTATCAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtttggccca ... caatatgcagGAGAAGAAAACTATTCGCCCTACATTTTCAGCTGAACGTATTTTTGGTGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgttggcatttatcaatattgtatcttctggtttgaatgatccaatatgcagGAGAAGAAAACTATTCGCCCTACATTTTCAGCTGAACGTATTTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGG
          atttatcaatattgta  TA-rich tract