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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatatgcttctgtttatttctgttcactctttaaaatatgtcgggcacctctttagctatatgtggattttcacaatctgaaatgtaatatcttaatgaacatagcaaggagtctgcctatttcagtttttacctacccactgggtttagaaagctggctgaatatttgctgatgcaaattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g65090.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G400604_T01 (Zea mays), 3'ss of exon 6
gtagatatgctt-ctgtttatttc--tgttcactctttaaaatatgtcgggcacctctttagctatatgtggattttcacaatctgaaatgtaatatcttaa-tgaacatagcaaggagtctg-cctatttcagttttta--cctacccactgggtttagaaagctggct---gaatatttgctgatgcaaattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG
||||||||  || || |||| ||   |   | ||||    ||    | | |||| |  |||||| ||| |  |||  |    ||  |||| | | |    |  |   || | | ||    ||    |||| ||      |  | |   || |  ||     ||    | |    |||||||| ||||| || ||||||||||||||||||||||||| ||||| ||||| |||||||||||||| ||||||||||||||||| |||||||||||||||||||||
gtagatatatttgctctttactttgttaccccctctcctgaaatgcttgtgcactttattagctttattt--attgcccttgtcataaatattagaatgcaccttttcagaactagatacctaatttattccaaaaccaaaacttggacattaagtaatataactaagttctgaaatatttgatgatggaacttttacagGCTTTTGCAATGACGGGTTGGCGTCTTGGTTACCTTGCAGCCCCTAAACATTTTGTTGCAGCATGTGGAAAGATCCAAAGCCAG

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA11G36190.1 (Glycine max), 3'ss of exon 6
gtagatatgcttctgtttatttctgttcactctttaaaatatgtcgggcacctctttagctatatgtggattttcacaatctgaaatgtaatatcttaatgaacatagcaaggagtctgcctatttcagtttttacctacccactgggtttagaaagctggctgaatatttgctgatgcaaattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG
                                                                          | | || | ||||    ||| |    |||  |       | | || | || |            |  |   |||| |  |        |||   ||| |   ||    | ||  || | ||||||||||| || ||||| ||||| ||  |||| |  ||||||||||||||||| || |||| |||||| |||||||||
--------------------------------------------------------------------------ctcgatgt-aaattctgtatttcgtagaatgtcttgtaaattatggcaatgtaga---------aagcctcgggtctgaatta-----tgatggttttcaactgtgt-tcttgtagACATTTGCAATGACTGGTTGGCGGCTTGGGTATATTGCTGGTCCAAAACATTTTGTTGCTGCATGTGAAAAGATTCAAAGCCAG

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G14720.1 (Glycine max), 3'ss of exon 6
gtagatatgcttctgtttatttctgttcactctttaaaatatgtcgggcacctctttagctatatgtggattttcacaatctgaaatgtaatatcttaatgaacatagcaaggagtctgcctattt--cagtttttacctacccac-tgg--gtttagaaagctggctg-aatatttgctgatgcaaattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG
                                                          | ||  | || | | |   | |      ||| |    ||   | |  ||     || ||  | |  ||     |  | |  | ||||| |||  |  |  |||  ||  |   | | ||           || || |||| ||||||||||| || ||||| ||||||||  |||| |  |||||||||||||||||||| ||||||||||||||||| |||
----------------------------------------------------------gtta-gtctgtaatgttctatttc----tgttaagagttgccggatgtattgttgattcctcattcttatttatactcaattgcccacatggaagcctccaaatttgattatgacacttttgagctgtttttctatagGCCTTTGCAATGACTGGTTGGCGGCTTGGATATATTGCTGGTCCAAAACATTTTGTTGCAGCATGTGGAAAGATCCAAAGTCAG

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA05G31490.2 (Glycine max), 3'ss of exon 6
gtagatatgcttctgtttatttctgttcactctt-taaaatatgtcgggcacctctttagctatatgtggattttcacaatctgaaatgtaatatcttaatgaacatagcaaggagtctgcctatttcagtttttacctacccactgggtttagaaagctggctg-aatatttgctgatgcaaattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG
||   | ||      | |||||||||| |   ||     || | | |   | | ||        ||    |||||   |  ||||| ||     |||| ||    ||||  ||     | |  |||| ||   | || |        ||  |  |||  ||  |   | | ||           |  || |||| ||||||||||| || ||||| ||||||||  |||| |  |||||||||||||||||||| ||||||||||||||||| |||
gttagtctgtaatgttctatttctgttaagagttgcgggatgtattgttgatccctc-------attcttatttt---atactgaattgcctattctttatttcaatagtgag-----ttctaattttagacatgacatgg-----aggcctccaaatttgattatgacacttttgagctgttttcctatagGCCTTTGCAATGACTGGTTGGCGGCTTGGATATATTGCTGGTCCAAAACATTTTGTTGCAGCATGTGGAAAGATCCAAAGTCAG

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA18G02250.1 (Glycine max), 3'ss of exon 6
gtagatatgcttctgtttatttctgttcactctttaaaatatgtcgggcacctctttagctatatgtggattttcacaatctgaaatgtaatatcttaatgaacatagcaaggagtctgcctatttcagtttttacctacccactgggtttagaaagctggctgaatatttgctgatgcaaattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG
                                                                                                                                                          |||     ||| |  ||    ||     | ||  || | ||||||||||| || ||||| ||||| ||  ||||    |||||||||||||||||||| |  |||||||| |||||||||
-------------------------------------------------------------------------------------------------------------------------------------------------------gtcaagtcttatga-tgcttttcaattgtggtcttgtagACATTTGCAATGACTGGTTGGCGGCTTGGGTATATTGCTTGTCCAAAACATTTTGTTGCAGCATTCGGAAAGATTCAAAGCCAG

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA11G36200.1 (Glycine max), 3'ss of exon 7
gtagatatgcttctgtttatttctgttcactctttaaaatatgtcgggcacctctttagctatatgtggattttcacaatctgaaatgtaatatcttaatgaacatagcaaggagtctgcctatttcagtttttacctacccactgggtttagaaagctggctgaatatt--tgctgatgcaaattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG
                                                                                      |      ||  |||    ||      || | |   ||| |     |||  | |   |    |  |  ||  ||| || |  |||  |    ||     | ||  || | ||||||||||| || ||||| ||||| ||| |||| |   ||||||||||||||||||| || |||||||| ||||| |||
--------------------------------------------------------------------------------------tactcagtccaaatctgtattttttagaatgtttgtatgt-----tttgacaatgtagaaagcctc-aagtctgtcttacgattgttttcaattgtgttattgtagACATTTGCAATGACTGGTTGGCGGCTTGGGTACATTGCTGGTACAAAACATTTTGTTGCAGCATGCGGAAAGATTCAAAGTCAG

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G14720.3 (Glycine max), 3'ss of exon 6
gtagatatgcttctgtttatttctgttcactctttaaaatatgtcgggcacctctttagctatatgtggattttcacaatctgaaatgtaatatcttaatgaacatagcaaggagtctgcctattt--cagtttttacctacccac-tgg--gtttagaaagctggctg-aatatttgctgatgcaaattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG----------------
                                                          | ||  | || | | |   | |      ||| |    ||   | |  ||     || ||  | |  ||     |  | |  | ||||| |||  |  |  |||  ||  |   | | ||           || || |||| ||||||||||| || ||||| ||||||||  |||| |  |||||||||||||||||||| ||||||||||||||||| |||                
----------------------------------------------------------gtta-gtctgtaatgttctatttc----tgttaagagttgccggatgtattgttgattcctcattcttatttatactcaattgcccacatggaagcctccaaatttgattatgacacttttgagctgtttttctatagGCCTTTGCAATGACTGGTTGGCGGCTTGGATATATTGCTGGTCCAAAACATTTTGTTGCAGCATGTGGAAAGATCCAAAGTCAGGTATGCTACATTTTTT

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv18s0001g04860.t01 (Vitis vinifera), 3'ss of exon 6
gtagatatgcttctgtttatttctgttcactctttaaaatatgtcgggcacctctttagctatatgtggattttcacaatctgaaatgtaatatcttaatgaacatagcaagg-agtctgcctatttcagtttttacctacccactgggtttagaaagctggctgaatatttgctgatgcaaattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG
                                                                            || | | |||||||| |   |    | || ||||  | ||  |  ||||    |     ||     |  ||    | ||||      |  | ||| |    ||  |  ||| ||| ||||||||||||| || ||||||||||||||||| || |  |||||||| ||||| ||||| |||||||| || || ||||||
----------------------------------------------------------------------------cattgtaaaatgtaaaactattgc-atcacagcactgtaggttatctataatggg----acaggttctttg----tggaaa------ttgacattagaatgtggcacatttgcagACTTTTGCAATGACTGGTTGGCGACTTGGATACCTAGCTGGTCCAAAACACTTTGTGGCAGCATGTGGAAAAATTCAGAGCCAG

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|29686132|gb|CB682407.1|CB682407
EST:     GGATAGAACATTAACTGTAAATGGTTTTTCTAAG                         GCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACAT
genomic: GGATAGAACATTAACTGTAAATGGTTTTTCTAAGgtagatatgc ... aattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACAT
EST: gi|428197|gb|D24345.1|D24345
EST:     CATTGCCTGGNATGTGGGATAGAACATTAACTGTAAATGGTTTTTCTAAG                         GCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACAT
genomic: CATTGCCTGGAATGTGGGATAGAACATTAACTGTAAATGGTTTTTCTAAGgtagatatgc ... aattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACAT
EST: gi|29644554|gb|CB649561.1|CB649561
EST:     CATTGCCTGGAATGTGGGATAGAACATTAACTGTAAATGGTTTTTCTAAG                         GCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACAT
genomic: CATTGCCTGGAATGTGGGATAGAACATTAACTGTAAATGGTTTTTCTAAGgtagatatgc ... aattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACAT
EST: gi|86849106|gb|CI295847.1|CI295847
EST:     CATTGCCTGGAATGTGGGATAGAACATTAACTGTAAATGGTTTTTCTAAG                         GCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACAT
genomic: CATTGCCTGGAATGTGGGATAGAACATTAACTGTAAATGGTTTTTCTAAGgtagatatgc ... aattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACAT
EST: gi|29645872|gb|CB650879.1|CB650879
EST:     CATTGCCTGGAATGTGGGATAGAACATTAACTGTAAATGGTTTTTCTAAG                         GCTTTTGCAATGACGGGCTGGCG
genomic: CATTGCCTGGAATGTGGGATAGAACATTAACTGTAAATGGTTTTTCTAAGgtagatatgc ... aattttacagGCTTTTGCAATGACGGGCTGGCG
EST: gi|29683532|gb|CB679807.1|CB679807
EST:     CATTGCCTGGAATGTGGGATAGAACATTAACTGTAAATGGTTTTTCTAAG                         GCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACAT
genomic: CATTGCCTGGAATGTGGGATAGAACATTAACTGTAAATGGTTTTTCTAAGgtagatatgc ... aattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACAT
EST: gi|29679352|gb|CB675627.1|CB675627
EST:     CATTGCCTGGAATGTGGGATAGAACATTAACTGTAAATGGTTTTTCTAAG                         GCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACAT
genomic: CATTGCCTGGAATGTGGGATAGAACATTAACTGTAAATGGTTTTTCTAAGgtagatatgc ... aattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctacccactgggtttagaaagctggctgaatatttgctgatgcaaattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG
                                   tgctgat  putative branch site (score: 3)
                                            aaattttaca  TA-rich tract