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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttatattgggcgtttactgctgtattctcttcacactcaactaggttaggtaagcatgctgatcagcgaaatattttctccaaagCTTCAGATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACC

Basic information

species Oryza sativa
transcript LOC_Os05g38270.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38270.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA18G40600.1 (Glycine max), 3'ss of exon 7
-------------------gtaacttatattgggcgtttactgctgtattc---tcttcacactcaactaggttaggtaagcatgctgatcagcgaaatattttctccaaagCTT-CAGATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACC
                    ||  |  | |||   ||| | ||  ||||     | |  |   |     | || | | |||    |||||  ||   |||||||  || ||| || ||||| | || ||||||||||||||||||||||| || |||||||| ||||| || || ||| || |   ||  || || ||||| ||||  |||| 
gttggctcttgtggttacattatgtagttttgtaggttcaatgaagtatgaagatatggaaggtttttgatgtaaagcaagacacctgat--gcatcatatttttaccgaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGCTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGGGTAAAGATGGTATCATCCCCTCATCTTATAC-

upper sequence: LOC_Os05g38270.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G16400.1 (Glycine max), 3'ss of exon 6
-------------------gtaacttatattgggcgtttactgctgtattctcttcacactcaact---aggttaggtaagcatgctgatcagcgaaatattttctccaaagCTT-CAGATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACC
                    ||  |  | |||   ||| | ||  ||||     | |   |    |   | || | | |||    |||||  ||   |||||||  |||||| || ||||| | || ||||||||||||||||| ||||| || |||||||| ||||| || || ||| |  |   ||  || || ||||| ||||  |||| 
gttgcctcttgtggttacattatatagttttgtaggttcaatgaagtatgaagataaggatggtttttgatgtaaagcaagacacctgat--gcatcatatttttaccaaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGTTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGAGTAAAGATGGTATCATCCCCTCATCTTATAC-

upper sequence: LOC_Os05g38270.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------------------gtaacttatattgggcgttta-ctgctgtatt-ctcttcacactcaactaggttaggtaagcatgctga------tcagcgaa-atattttctccaaagCTTCAGATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACC------
                                                                 ||   |||  |   | |||   ||  | ||  || ||    ||     || | || || |||| |  |      |||  ||   || |||     ||| ||||||| | || ||||| |||||||||||||||||||| ||||| || || ||||| || ||||| || || |  || ||||| || ||||   | ||      
gtattgactttattatgggctatttgtcaacctaggtctaaaattttatctatgctattttcgtatataatatgataatcttttggttgaagcataactttttgtgctatggaagatcagttatgcattcgaagacatgtcattgattgtaattttctggaagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT

upper sequence: LOC_Os05g38270.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA18G03870.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------------gtaa-cttatattgggcgtttactgctgtattctcttcacactcaactaggttaggtaag-catgctgatcagcgaaatattttctccaaagCTTCAGATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACC------
                                                                         ||| ||| |  | |  |   |    | | |  | |  |   |||  || |  |  |||| ||||    | |  | ||| || | |    || ||||||| | || ||||| |||||||||||||||||||| ||||| || || ||||| || ||||| || || |  || ||||| || ||||   | ||      
gtattgactttattatgaactatttgtcaacctaggtctaaaattttatctgttattttcgtatatgatgtgataatcttttggttgaagcagaactttttgtgttatggaagatcagttatgcaatctaagacatgtcattgattgtaattttctgt---gagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT

upper sequence: LOC_Os05g38270.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv13s0019g02280.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------------------------------------------gtaacttatattgggcgtt--tactgctgtattctcttcacactcaactaggttaggtaagcatgctgatcagcgaaatattttctccaaagCTTCAGATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACC------
                                                                           | ||| ||   |||   |   ||   ||  |  |  |  |   || | |  || | | ||  |   | ||       || | ||| || ||| ||||||| |||| ||||| ||||||||||||||||| || || || ||||||||||| || ||  |||| || |  || ||||| || |||||  | ||      
gtaaatccatgaaatcttggattgttgtccctaagcctcagttttaattcatagttctttttctgttgtggttatgcaacataggctggtactcagtatgactagaagccatggaagttctattttgtaaagcaacaaacttaatgttttctat-tgttcccccaagtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTTTGGGTTCCCGGATACGTATGGTATCCTCTCCTCATCCTGTGCCTTGTGT

upper sequence: LOC_Os05g38270.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv08s0007g00930.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------------------gtaacttatattgggcgtttactgctgtattctcttcacactca--------actaggttaggtaagcatgctgatc---agcgaaatat----tttctccaaagCTTCAGATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACC------
                                                          | || || |  |  | | ||||  || |||  | ||     |||        || | | || | |||     | ||    ||| | | |     |||  | |||| ||||||| | || ||||| ||||||||||||||||| || ||||| || |||||||| || ||| |||    |   || || || || |||| ||||||      
gtaaattctccatcccctgggtcactgcagcccacacaagccacagttttcaggtgtagcaatttcttctttgtggttac-actatatagttttgtaggtcatttgaagtacgaagctatggaagatctttaatgtaaagcaagacacctaatttaacaaaagtttcagATATGGGACAGGTGTGGGGTTGGGGCTATGGAGGCGAAGGGCAGCTAGGTTTGGGTTCTCGGACAAAGCTGGTGTCTTCTCCTCATCTCATACCTTGCTT

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|29665759|gb|CB662034.1|CB662034
EST:     GAAGATAGTGGAAGTAGCTGCAGGTGGCCGTCATACATTAGTGCTGTCAG                         CTTCAGATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAAC
genomic: GAAGATAGTGGAAGTAGCTGCAGGTGGCCGTCATACATTAGTGCTGTCAGgtaacttata ... ttctccaaagCTTCAGATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacactcaactaggttaggtaagcatgctgatcagcgaaatattttctccaaagCTTCAGATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACC
                          tgctgat  putative branch site (score: 3)
                                         tattttctcc  putative PPT
                                      aaatattttct  TA-rich tract