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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_Os01g65090.1
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 63 (downstream exon)
Score: 30

GATTTATGAGCATATCATCTATCAGCCAGCAAAACACACAAGCTTTGCTTCATTGCCTGGAATGTGGGATAGAACATTAACTGTAAATGGTTTTTCTAAGgtagatatgc ... aattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctacccactgggtttagaaagctggctgaatatttgctgatgcaaattttacagGCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG
                                   tgctgat  putative branch site (score: 30)
                                            aaattttaca  TA-rich tract