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'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgagctcatactctgtttgttactgatagataacacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA

Basic information

species Oryza sativa
transcript LOC_Os04g51610.3
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 27
--gtttgagctcatactctgtttgttactgatagataacacggaagttatggttaatattctctc--------tcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
    |   |  |||  || | | || | |  || | |     |||| | | ||   | |  | |         |  |    || |     ||| ||||||| |  |||||||||||||||| ||||| ||| ||||||| |||||| |||||||||||||||||||  ||||||||||| ||||||| ||||| || ||||
tcagtcctgtgcatgttcagatagt-atttctaaaaagatgtgaagatgtagtctctgtagtgttgggtaaaattctaatttttgctcccttgtctggcagTTGTTGTGGGTTAACCTAATTATGGACACTTTGGGTGCCCTTGCATTGGCGACAGAACCACCTACAAACCATCTTATGGAGAGACCCCCAGTAGGGAGAA

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 27
---------------------------------------------------------------gtttgagctcatac---tctgtttgt-tactgatag-ataacacggaagttatggttaatatt-ctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
                                                               | |  |  |  | |   |||||   | | | || || ||  |    |||   || ||  |     |||   |||||||        ||||||| ||| | ||||||||||||||||| ||||||||| ||||||| |||||| |||||||||||||||||||  ||||||||||| ||||||| ||||| || ||||
gtttgagttcagctctgagatctattggtagttgcactatttatcatcatttaacttgtaaaagctgcaatttcttcagttctgtgcatgtccagacagtatttctaaaaagacgtgtttggtggaattctaatttttgct-----cccttggctgacagTTGCTGTGGGTTAACCTAATTATGGATACTTTGGGTGCCCTTGCATTGGCGACAGAACCACCTACAAACCATCTTATGGAGAGACCCCCAGTAGGGAGAA

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 28
---gtttgagctcatactctgtttgttac-----tgat--agataacacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
      ||  |||  |   ||||   |       ||||  | || |||   |   |    || | | |  ||   |||  |     |||  ||  |   ||||  ||||||| ||||| |||||||| || || || |||||||||||||| || ||||| || || ||| | |||||||| ||| ||||||||||| |||
gtaccctgccctctaatattgttgaatgaatatatgattcaaattacagatagagtcacatttacaatacctgcgtttacccctctcttactgtgta-tagCTTTTGTGGGTCAACCTTATCATGGACACACTTGGGGCTCTTGCACTGGCTACGGAACCGCCAACAGACAACCTTATGCACAGATCACCAGTTGGCCGAA

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 28
-----gtttgagctcatactctgtttgttactgatagataacacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
      |      ||||  ||| ||  | | |  || || | | |      ||    |        || | ||| |         || |     ||||  ||||||| ||| | |||||||| || || || |||||||||||||| || ||||| || || ||| | |||||||| ||| ||||||||||| |||
gtaccctgcattgtcatcttctattgttgaatagtatatgatatgattcaaataacaagataagagtcacatttacaatattcgatttgtgtatagCTTTTGTGGGTCAACGTTATCATGGACACACTTGGGGCTCTTGCACTGGCTACGGAACCGCCAACAGACAACCTTATGCACAGATCACCAGTTGGCCGAA

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 26
---------gtttga--gct-catactctgtttgttactgatagataacacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
         |  |||  | | | |||   | | | |    |     | ||  |||   | |||  || ||   | | |  || |   |||  | ||    |||||  ||||||| ||||| ||||||||||| || || || ||||||||||| || ||||| || || ||||  || ||||| ||| ||||||||||| |||
aaaaactaagactgatagttacgtacaagggtagattaaaaacatcatcaatgaaaaaaaggtatat-tttggtttttgatgttcatgctcttgggt--acagCTTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 29
gtttgagctcatactctgtttgttactgatagata-acacggaagttatggttaatat---------tctctctcttttgcttgggcttgttggctgg--cagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
     |    |    ||| |  ||||  | |     | |   || | ||  | |||           | |||   |||| | ||  | || |    ||  |||||  ||||||||||||| ||||||||||| || || || ||||||||||| || |||||||| || ||||  || ||||| ||| ||||||||||| |||
---ataaaaaactgactgataattacgtacaagggcagattaaaatcatcatcaatgaaaaaaggtatatcttggtttttcatgttcatgctcttgggtacagCTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCACCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 26
gtttgagctcatactctgtttgttactgatagataacacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
      | |  |||  || |  ||| |  |  ||          ||| |   |  ||      | |  || |   | |  |||    |||||| || ||||| ||||| |||||||||||||| || || |||||||| || ||||| ||||| || || ||||||||||| ||| | || ||||| ||||
------gttagtaccttgatgcttatt--tgaatggttgaacttttaagacaaggataaaagatataatggt---gttctttgat--gcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 28
-----gtttgagctcatactctgtttg---ttactgatagataa---cacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
     ||   |  |  | || |   ||   || |  |||   ||    | |||   | |  ||  | ||   || ||||| |||       ||||    ||||| || ||||||||||| |||||||||||||| || || |||||| |||| || |||||||| ||||| ||||||||| | ||| | ||||||||  |||
gcagtgtgaaaaatgttgcttttcatggtctttcaaataaccaaatttagggattatttaattcttcttacatcactttttcttttctcacttggt--acagCTTCTATGGGTTAACCTTATCATGGATACTCTTGGAGCACTTGCATTGGCTACTGAACCACCAACTGATCATCTTATGGAAAGATCTCCAGTTGGTCGAA

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 29
gtttg-agctcatactctgtttgttactgatagataacacggaagttatggt-taatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
||| |  || ||  |  || |   |  |||  | | |||      |||||   |   |||   |    | ||  | | ||  || |||  ||||| || |||||||| || |||||||||||||| || || |||||| |||| || |||||||| || || || || ||||| || || ||||||||  |||
gttggtggcccacccattgctgcctcttga--gttgacagttctattatgtcgtctcatttgtttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA

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|88351169|gb|CI623391.1|CI623391
EST:     AAGTTGTTGCTGCTGTCAGTTCTGGGAATGTTCCCCTGAACGCTGTTCAG                         CTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCG
genomic: ACGTTGTTGCTGCTGTCAGTTCTGGGAATGTTCCCCTGAACGCTGTTCAGgtttgagctc ... tggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCG
EST: gi|58594188|gb|CF992496.1|CF992496
EST:     CGTTGTTGCTGCTGTCAGTTCTGGGAATGTTCCCCTGCAACGCTTTTCAG                         CTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCG
genomic: CGTTGTTGCTGCTGTCAGTTCTGGGAATGTTCCCCTG-AACGCTGTTCAGgtttgagctc ... tggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCG
EST: gi|218500877|gb|FG965670.1|FG965670
EST:     ACGTTGTTGCTGCTGTCAGTTCTGGGAATGTACCCCTGAACGCTGTTCAG                         CTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCG
genomic: ACGTTGTTGCTGCTGTCAGTTCTGGGAATGTTCCCCTGAACGCTGTTCAGgtttgagctc ... tggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
            ggttaat  putative branch site (score: 4)
        ttatggttaatatt  TA-rich tract