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

gtaactatggtatttcgtttatgatggtatttatgtaggattattcccaaattattcttacctgagttttcctgctgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC

Basic information

species Oryza sativa
transcript LOC_Os05g29050.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g29050.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 9
gtaactatggtatttcgtttatga-tggtatttatgtaggattattcc-caaattattcttacctgagttttcctgctgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC
         |||||| |||  |   |  ||   ||  ||   |||    |||| |      |  | | ||   || ||||| ||| |||||||||| || ||||||||||||||||| ||||||||||||||||||||    |||||||| ||||||||||||||||||||||||||||||||||| 
---------gtattttgttgttatcttctacccattcagatgtatggggcaaagtccctaaatgtcacttcatct-ctgtaaata-gGGAATCTGAACCCAATTCCTGGGAGGACACCATGAAAGATGAGCTGGACCGTGATAAATATCCCCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAT

upper sequence: LOC_Os05g29050.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 10
----------gtaactatggtatttcgtttatgatggtatttatgtaggattattcccaaattattct-------tacctgagttttcctgctgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC
          ||   || | ||| || || || ||   ||| ||    || ||   |     | |||        ||   || |  |  |    |     || |||||||| |||||||| ||||| || ||||||||||||||  | || ||    ||||||||||| |||||||||||||||||||| ||||| || |  
cactttgaatgtg-ttaagatatgtcattcattatta-attgatcatagactagctctttcctgttcaacgatagtaatagattcattttcaattttgacagAGAATCTGAACCAAATTCATGGGAAGATACAATGAAAGATGAATTAGAACGTGAAAAATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGG

upper sequence: LOC_Os05g29050.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 10
-------gtaactatggta---tttcgtttatgatgg--tatttatgtaggattattcccaaattattcttacctgagttttcctgctgtacata---agGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC
        | | | || ||   | || || || ||    || | ||  |    | || ||   | |   |||      | ||| |  |  |  |    || |||||||| || ||||| ||||| || ||||||||||||||  | || ||    ||||||||||| |||||||||||||||||||| ||||| || |  
ttgcactttgaatgtgttaagatgtcattcatcattaattaatcatagacagctctttcctgctgaacgttagtaatatattcattttcaattttgacagAGAATCTGAACCTAATTCATGGGAAGATACAATGAAAGATGAATTAGAACGTGAAAAATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGG

upper sequence: LOC_Os05g29050.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA20G38200.1 (Glycine max), 3'ss of exon 11
--------gtaactatggta----tttcgtttatgatggtatttatgtaggattattcccaaattattcttacctgagtttt---cctgctgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC
         || |  || |      |||  |  || || |   | ||      ||    |  | || | |||  | | || |     || ||      || ||||||||||||||||| ||||| ||||| |||||||||||  |||| || | ||| ||||| || ||||| ||||| ||||| || |||||||| |  
cattacaattagccgtgttggagccttcactattgctgatgagtctgcttttctaagttcttagtaatattatataatttgtaattttgttggttgatagAGAATCTGAGCCAAATTCATGGGAAGACACCATGAAAGATGAATTGGATCGCAAGAAGTATCCCCGTATGCCATGGCACGATGTCCATTGTGCTCTTTGG

upper sequence: LOC_Os05g29050.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 11
-----------gtaactatggtatttcgtttatgatggtatt-tatgtaggattattcccaaattattc----ttacctgagttttcctg----ctgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC
            | || || || | |  |||   | |  |||  | ||  | ||   | |    | ||     ||   | | || |  ||     |  |  | ||||||||||| |||||||| ||||| || ||||||||||||||  |||| ||    ||||||||||| ||||| |||||||| || || ||||| || |  
gtgtgagaacattgacaatagtttcttcttttctaagtaattgcaagtttgttttcactctggctctttcacattggataacttgtaatgaattttcaatttcagGGAATCTGAACCAAATTCTTGGGAAGATACAATGAAAGATGAATTGGATCGTGGAAAATATCCTCGTATGCCATGGCATGACGTCCATTGTGCCCTATGG

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|58669537|gb|CK058223.1|CK058223
EST:     TCAGATGTTCCTCCTGTGATATGGCCA-GGAAAGACTACTATAACCCCAG                         GGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCG
genomic: TCAGATGTTCCTCCTGTGATATGGCCAGGGAAAGACTACTATAACCCCAGgtaactatgg ... tgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCG
EST: gi|58692366|gb|CK081053.1|CK081053
EST:     TCAGATGTTCCTCCTGTGATATGGCCAGGGAAAGACTACTATAACCCCAG                         GGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAG
genomic: TCAGATGTTCCTCCTGTGATATGGCCAGGGAAAGACTACTATAACCCCAGgtaactatgg ... tgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgtaggattattcccaaattattcttacctgagttttcctgctgtacataagGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC
                        ttcttac  putative branch site (score: 2)
                                    ttttcctgct  putative PPT
                  aaattattctta  TA-rich tract