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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaataaatccacaatgatccttttaaacctgtgctccattctgttgtacctggttgtatataatgcgtacatatattgacaaaattttgcatgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTCTCTCCATACCATTCTGACCGGTTTCTACTTTCCCC

Basic information

species Oryza sativa
transcript LOC_Os02g05340.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM5G816609_T01 (Zea mays), 3'ss of exon 7
gtaagttaataaatccacaatgatccttttaaacctgtgctccattctgttgtacctggttgtatataa--tgcgtacatatattgacaaaattttgcatgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTCTCTCCATACCATTCTGACCGGTTTCTACTTTCCCC
||||||  ||| ||| | ||||||| |||   | |  |  |  | | |    | | || |||| | | |  | | | | |  ||| |    ||| || |  |  |||||| ||||||||||| || ||||||||||| || ||||| |||||||| || ||||| |||||||||||  | ||||| ||||||||
gtaagt--atagatcgataatgatcatttggcatccttcatggacttttggttccttgattgttttttagtttcatgctttgattaattttattgtgtacatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCGTACCATTCTGATAGATTTCTTCTTTCCCC

upper sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G155384_T01 (Zea mays), 3'ss of exon 21
gtaagttaataaatccacaatgatccttttaaacctgtgctccattc-tgttg--tacctggttg---tatataatgcgtacatatattgacaaaattttgcatgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTCTCTCCATACCATTCTGACCGGTTTCTACTTTCCCC
        ||| ||| || | |||  |||   | |  |  |  | |  |  ||  | | |||||    ||||   | | | |||  ||       ||  ||   ||  |||||| |||||||| || || ||||| ||||| || ||||| |||||||| || |||||||||||||| ||  | ||||| || |||||
------gtatatatcaacgacgatattttggcatccttcatgtactaataatggttccttggtttcgttataagttccatccattgatccgttttatcgtgttcgtcgtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC

upper sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G155384_T02 (Zea mays), 3'ss of exon 21
gtaagttaataaatccacaatgatccttttaaacctgtgctccattc-tgttg--tacctggttg---tatataatgcgtacatatattgacaaaattttgcatgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTCTCTCCATACCATTCTGACCGGTTTCTACTTTCCCC
||||||  ||| ||| || | |||  |||   | |  |  |  | |  |  ||  | | |||||    ||||   | | | |||  ||       ||  ||   ||  |||||| |||||||| || || ||||| ||||| || ||||| |||||||| || |||||||||||||| ||  | ||||| || |||||
gtaagt--atatatcaacgacgatattttggcatccttcatgtactaataatggttccttggtttcgttataagttccatccattgatccgttttatcgtgttcgtcgtcagGTTAGAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC

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|88381509|gb|CI682165.1|CI682165
EST:     TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGT                         GTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
genomic: TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGTgtaagttaat ... atgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
EST: gi|58594042|gb|CF992350.1|CF992350
EST:     TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGT                         GTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
genomic: TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGTgtaagttaat ... atgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
EST: gi|29667415|gb|CB663690.1|CB663690
EST:     CATCTGTTTTGT                         GTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
genomic: CATCTGTTTTGTgtaagttaat ... atgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
EST: gi|88580211|gb|CI692213.1|CI692213
EST:     TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGT                         GTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
genomic: TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGTgtaagttaat ... atgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
EST: gi|88582162|gb|CI699549.1|CI699549
EST:     TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGT                         GTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
genomic: TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGTgtaagttaat ... atgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
EST: gi|38477734|gb|CF961867.1|CF961867
EST:     TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTCGT                         GTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTCGTTGACTCTC
genomic: TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGTgtaagttaat ... atgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
EST: gi|38471736|gb|CF955867.1|CF955867
EST:     TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGT                         GTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
genomic: TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGTgtaagttaat ... atgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
EST: gi|88580987|gb|CI697953.1|CI697953
EST:     TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGT                         GTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
genomic: TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGTgtaagttaat ... atgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
EST: gi|88369867|gb|CI680543.1|CI680543
EST:     TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGT                         GTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
genomic: TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGTgtaagttaat ... atgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
EST: gi|88592801|gb|CI710929.1|CI710929
EST:     TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGT                         GTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC
genomic: TTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGTgtaagttaat ... atgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTC

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: 73 (upstream exon), 70 (downstream exon)
Score: 50

ATTGGGTTTCATTGGTGCTGGTACAAACAATGCTAGAATAGCTGGTATGCTTCGCAATCTTTCAAGTTACTATTACAAAGAAGCTGCGCATCTGTTTTGTgtaagttaat ... atgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTCTCTCCATACCATTCTGACCGGTTTCTACTTTCCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacctggttgtatataatgcgtacatatattgacaaaattttgcatgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTCTCTCCATACCATTCTGACCGGTTTCTACTTTCCCC
                            tattgac  putative branch site (score: 50)
                      tacatatattgacaaa  TA-rich tract