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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGTTACTCACTCGGTGGGTAACTGTGTCAAGCGAGTGGTGGTCATTGTGACATCCGTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGGgtaagaatcattttctgttcacttctgtatcaaattgactgcatcgcacctcctttacatatccaaatatttgcgccctgcag

Basic information

species Oryza sativa
transcript LOC_Os09g12600.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g12600.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G103047_T01 (Zea mays), 5'ss of exon 8
CCTGTTACTCACTCGGTGGGTAACTGTGTCAAGCGAGTGGTGGTCATTGTGACATCCGTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGGgtaagaatcattttctgttcacttctgtatcaaattgactgcatcgcacctc--ctttacatatcc-aaatatttgcgccctgcag
|| || || || || ||||| || || |||||||| ||||||||||||||||| || |||||||||||| | ||||||||||| || |||||||| || |||  | ||| ||| || ||        || | | || | | | || |   ||  | | ||  ||   ||| |||       |||||
CCAGTCACACATTCAGTGGGCAATTGCGTCAAGCGTGTGGTGGTCATTGTGACCTCGGTTCTGTTCTTCAGGACCCCTGTTTCTCCCATCAACTCACTCGgtctgcatcttttccttttgctactcttaactattttattccgtcacggttcaccctcacgaatatgaaacattaaatttgtgcag

upper sequence: LOC_Os09g12600.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G047404_T01 (Zea mays), 5'ss of exon 8
CCTGTTACTCACTCGGTGGGTAACTGTGTCAAGCGAGTGGTGGTCATTGTGACATCCGTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGGgtaagaatcattttctgttcacttctgt--atcaaattgactgc---atcgcacctccttt-ac-atatccaaatatttgcgccctgcag
|| || || || || ||||| || || |||||||| ||||||||||||||||| || |||||||||||| | ||||||||||| || ||||||||||| |||  | ||| |||||  || ||| |  |  |  ||||  |       |||       || | || | ||  ||| |||     | |||||
CCAGTCACACATTCAGTGGGCAATTGCGTCAAGCGTGTGGTGGTCATTGTGACCTCTGTTCTGTTCTTCAGGACCCCTGTTTCTCCCATCAACTCTCTTGgtctgcatc-ttttcctttgactaccctcaactaaatcaatcattttatcatgttcactctcacgaaattgaaacattaaattcgtgcag
















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|88214697|gb|CI214546.1|CI214546
EST:     GACATCCGTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGG                         GAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
genomic: GACATCCGTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGGgtaagaatca ... cgccctgcagGAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
EST: gi|58662048|gb|CK050728.1|CK050728
EST:     GACATCCGTTCTGTTCTTCCGAACCCCTGTTTCGCCTATCAACTCTCTGG                         GAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
genomic: GACATCCGTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGGgtaagaatca ... cgccctgcagGAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
EST: gi|88254980|gb|CI353804.1|CI353804
EST:     CCCCTGTTTCGCCTATCAACTCTCTGG                         GAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAAGTGAAGCGGC
genomic: CCCCTGTTTCGCCTATCAACTCTCTGGgtaagaatca ... cgccctgcagGAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
EST: gi|88366076|gb|CI548323.1|CI548323
EST:     TCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGG                         GAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
genomic: TCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGGgtaagaatca ... cgccctgcagGAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
EST: gi|88276494|gb|CI397098.1|CI397098
EST:     CCCTGTTTCGCCTATC-ACTCTCTGG                         G-ACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
genomic: CCCTGTTTCGCCTATCAACTCTCTGGgtaagaatca ... cgccctgcagGAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
EST: gi|88468110|gb|CI517569.1|CI517569
EST:     GTTCTGTTGTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGG                         GAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
genomic: GTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGGgtaagaatca ... cgccctgcagGAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
EST: gi|88247773|gb|CI247622.1|CI247622
EST:     GACATCCGTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGG                         GAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
genomic: GACATCCGTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGGgtaagaatca ... cgccctgcagGAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
EST: gi|89180351|gb|CI044630.1|CI044630
EST:     GACATCCGTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGG                         GAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
genomic: GACATCCGTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGGgtaagaatca ... cgccctgcagGAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
EST: gi|88273727|gb|CI394133.1|CI394133
EST:     GACATCCGTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGG                         GAACCGGAGTCGCTCTTGCCGGAGTGTTCCGGTACTCACAATTGAAGCGGC
genomic: GACATCCGTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGGgtaagaatca ... cgccctgcagGAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
EST: gi|88247742|gb|CI247591.1|CI247591
EST:     GACATCCGTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGG                         GAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
genomic: GACATCCGTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGGgtaagaatca ... cgccctgcagGAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGC
EST: gi|88978323|gb|CI384744.1|CI384744
EST:     GACATCCATTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGG                         GAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAAATTGAAGCGG
genomic: GACATCCGTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGGgtaagaatca ... cgccctgcagGAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAA-TTGAAGCGG

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), 60 (downstream exon)
Score: 47

CCTGTTACTCACTCGGTGGGTAACTGTGTCAAGCGAGTGGTGGTCATTGTGACATCCGTTCTGTTCTTCCGCACCCCTGTTTCGCCTATCAACTCTCTGGgtaagaatca ... cgccctgcagGAACCGGAGTCGCTCTTGCCGGAGTTTTCCTGTACTCACAATTGAAGCGGCTTAAACCCAAGCCCAAGACTGCCTGATTGTGTCTTGGTATCTATCGTGA




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