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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAATCTCTTTCTCCTGATGTGCCTCTGTACAAAGTCGTTGAAGGGAATGAACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctattggatatttaccactatatctttttttctcagttctatcaattggaactttgtatttaagagatttcaccttggaagcaatttttcgtata...

Basic information

species Oryza sativa
transcript LOC_Os03g24220.2
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24220.2 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G081322_T01 (Zea mays), 5'ss of exon 20
CGAATCTCTTTCTCCTGATGTGCCTCTGTACAAAGTCGTTGAAGGGAATGAACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctattggatatttaccactatatctttttttctcagttctatcaattgga-actttgtatttaagagatttcaccttggaagcaatttttcgtata
 |||  | ||||||||||||||||||| || ||||||  ||||||||||||||| ||||||||||| || |||||||||||||||| | || |||| |||||||||| ||  ||||||||  || ||| ||      |||| | |      |    |  ||   ||||  || | |     ||| | ||  |  |  | | 
TGAAGGTATTTCTCCTGATGTGCCTCTCTATAAAGTCAATGAAGGGAATGAACCTTGCTTCTTCAGGACATACTTCTCCTGGGATAGCGCACGATCCGTGgtatgctcttatatatttacttctgtattttaaaagttcagcttttcgttctaagtatgttccgtttattaggtatttgtatggta-cagatcatattttg

upper sequence: LOC_Os03g24220.2 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G359566_T01 (Zea mays), 5'ss of exon 4
CGAATCTCTTTCTCCTGATGTGCCTCTGTACAAAGTCGTTGAAGGGAATGAACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctattggatatttaccactatatctttttttctcagttcta---tcaattggaactttgtatttaagagatttcaccttggaagcaatttttcgtata
 |||    ||||||||||||||||||| || ||||||  ||||||||||||||| ||||||||||| || | |||||||||||||| |||| | ||  ||||||||| || |||||||||   | ||| || |    |||| | |    | || |     |||||||   |  | |      ||| | |      ||  |   
TGAAGGAATTTCTCCTGATGTGCCTCTCTATAAAGTCAATGAAGGGAATGAACCTTGCTTCTTCAGGACATTCTTCTCCTGGGATAGCACACGGTCCCTGgtatgctcttagatatttacttttgtattttataagttcagcttttcgtttaactatgtatttgtatcggacggctgatgttttgaaggtttaccttttt---

upper sequence: LOC_Os03g24220.2 (Oryza sativa), 5'ss of exon 19
lower sequence: AT2G41740.1 (Arabidopsis thaliana), 5'ss of exon 19
CGAATCTCTTTCTCCTGATGTGCCTCTGTACAAAGTCGTTGAAGGGAATGAACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctattggatatttaccactatatctttttttctcagttctatcaattggaactttgtatttaagagatttcaccttggaagcaatttttcgtata-------------------------------------------
 |||    |   |||| | || ||  | |||||| ||  ||||||||| ||||||||||||||||  |||||||| || ||||||  ||| | | || | ||| |  | |   | || |  |    || |   |     |  |  || | |  |||  ||  |  | |  |||||| | ||        | |||| | |                                            
GGAAGGCTTGCATCCTAAAGTCCCAATCTACAAAATCAATGAAGGGAACGAACCATGCTTCTTCACCACTTACTTTTCTTGGGATGCCACTAAAGCTATCgtaagtgacttagtgttgaagaggg-atttagataatataactagataactctgaatgtt--acctcatggatttc-ctttactgtttctctttcttttctccttgaatttacctttcttctgttttaaacattgggatatag

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|88694289|gb|CI738327.1|CI738327
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|58596217|gb|CK006745.1|CK006745
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|218486625|gb|FG969617.1|FG969617
EST:     CAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: CAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|58677092|gb|CK065779.1|CK065779
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|25798468|gb|CA754429.1|CA754429
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGNGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAACTTTCACTTCTTTTCGGGATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|396941448|gb|HO188657.1|HO188657
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|29669712|gb|CB665987.1|CB665987
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|88718464|gb|CI741974.1|CI741974
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGTTCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|58661440|gb|CK050120.1|CK050120
EST:     AACCATGCTTCTTCAGAACTTACGGCGCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|33674859|gb|CF303098.1|CF303098
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGNGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|58674368|gb|CK063054.1|CK063054
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|58673715|gb|CK062401.1|CK062401
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|58610643|gb|CK038355.1|CK038355
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|56157785|gb|C26501.2|C26501
EST:     ACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: ACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|58672631|gb|CK061317.1|CK061317
EST:     TGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: TGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|58612287|gb|CK039999.1|CK039999
EST:     CAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: CAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|58652765|gb|CK041445.1|CK041445
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC

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: 72 (upstream exon), 57 (downstream exon)
Score: 44

CGAATCTCTTTCTCCTGATGTGCCTCTGTACAAAGTCGTTGAAGGGAATGAACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG




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