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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgcttctataactgttttaagtctgaagcagtaggaattcattgtgtttactttctttgcaaattacagtagttatctattttctcgttatgccc...

Basic information

species Oryza sativa
transcript LOC_Os04g52370.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G044629_T02 (Zea mays), 5'ss of exon 11
--------------------------------ATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgct------tctataactgttttaagtctgaa--gcagtaggaattca--ttgtgtttactttctttgcaaattacagtagtt--atctattttctcgttatgccc------------------
                                || ||| |||| ||||||||| |||| || ||||| ||||| ||||||||||||||||||||||||  ||||||| |      | |    |||  ||   ||  ||  || || |  | |||     ||     |    | |  ||   ||   |||  | ||   |    ||| ||                     
AAACTGTTCTCTCCTTTTTTTTTTTTTTGTAGATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttgtctagtttgcctctgccttctctccaaaatgccgtcgccagtcaggccttgagcgatagagtaggcaaccgcatctgttggacctgcctgacagttgtgtgtcgtcgatcttgtgagcag

upper sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G019986_T02 (Zea mays), 5'ss of exon 3
--------------------------------ATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgcttctataactgttttaagtctgaagcagtaggaattcattgtgtttactttctttgcaaattacagtagttatctattttctcgttatgccc-----------------------
                                || ||| |||| ||||||||| |||| || ||||| ||||| || |||||||| ||||||||||||  ||||||    |  |     |  |  | ||   |    ||  |||           |    |   | |  || |||||  | | |  ||      |||                          
CCTCTCTCTCTCTCGTTTTCCCCCTCCCCTAGATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatccccgtgttcttggttcgcct--tgtttcagagatttgcaagccaggcagcttcaacga--tagagtaggcaaccacgtttgttacatgagggtttgtgtatcttgtgtgaccag

upper sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G044629_T03 (Zea mays), 5'ss of exon 11
ATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgct------tctataactgttttaagtctgaa--gcagtaggaattca--ttgtgtttactttctttgcaaattacagtagtt--atctattttctcgttatgccc------------------
|| ||| |||| ||||||||| |||| || ||||| ||||| ||||||||||||||||||||||||  ||||||| |      | |    |||  ||   ||  ||  || || |  | |||     ||     |    | |  ||   ||   |||  | ||   |    ||| ||                     
ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttgtctagtttgcctctgccttctctccaaaatgccgtcgccagtcaggccttgagcgatagagtaggcaaccgcatctgttggacctgcctgacagttgtgtgtcgtcgatcttgtgagcag

upper sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G019986_T04 (Zea mays), 5'ss of exon 12
ATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgcttctataactgttttaagtctgaagcagtaggaattcattgtgtttactttctttgcaaattacagtagttatctattttctcgttatgccc-----------------------
|| ||| |||| ||||||||| |||| || ||||| ||||| || |||||||| ||||||||||||  ||||||    |  |     |  |  | ||   |    ||  |||           |    |   | |  || |||||  | | |  ||      |||                          
ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatccccgtgttcttggttcgcct--tgtttcagagatttgcaagccaggcagcttcaacga--tagagtaggcaaccacgtttgttacatgagggtttgtgtatcttgtgtgaccag

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|3768106|gb|AU032133.1|AU032133
EST:     ACTTTGGATTTTTTGAATCAAGTAGCANACAGCCTTGAGANGGACAGTAC                         TTATCATNTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
genomic: ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgctt ... ttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
EST: gi|88389670|gb|CI603169.1|CI603169
EST:     ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTAC                         TTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
genomic: ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgctt ... ttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
EST: gi|396941374|gb|HO188583.1|HO188583
EST:     ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAAGACAGTAC                         TTATCATCTTGCTGA
genomic: ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgctt ... ttgtgtccagTTATCATCTTGCTGA
EST: gi|88961150|gb|CI096554.1|CI096554
EST:     AGCCTTGAGAAGGACAGTAC                         TTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
genomic: AGCCTTGAGAAGGACAGTACgtgagtgctt ... ttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
EST: gi|86831371|gb|CI297640.1|CI297640
EST:     ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTAC                         TTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
genomic: ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgctt ... ttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG

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: 40 (upstream exon), 47 (downstream exon)
Score: 11

ATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgctt ... ttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGGCTTGAAGCTTGAACAGTATATATTCGACGCGTTCAGTTACTCCCCATCC




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