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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCGCTTTCATTTCCAGATCTCATATCAACACTTCCACAAATTGGGCTCCGAGGACTTTATCGGGGTTCTATCCCCGCAATTCTTGGTCAGTTTTCAAGgttagtgtcaattcagagttttagaggcaaatttgaatgtaggctgcaaattcacatcctgccatttgcag

Basic information

species Oryza sativa
transcript LOC_Os11g01270.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01270.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G146378_T02 (Zea mays), 5'ss of exon 1
CTTCGCTTTCATTTCCAGATCTCATATCAACACTTCCACAAATTGGGCTCCGAGGACTTTATCGGGGTTCTATCCCCGCAATTCTTGGTCAGTTTTCAAGgttagtgtcaattcagagttttagaggcaaatttgaatgtaggctgcaaa-ttcacatcctgccatttgcag
|| | || |||||||| || ||||| ||||  |||||||||||||| || |||||| | ||||| ||||||||||| |||||||| || |||||||||||||  |||  | |||| || |||| | |||||| |   ||||||||  ||| |||| |||||| |||||||||
CTACACTCTCATTTCCCGAGCTCATTTCAAAGCTTCCACAAATTGGACTTCGAGGATTGTATCGAGGTTCTATCCCAGCAATTCTCGGCCAGTTTTCAAGgtatgtggtatttcataggtttatatgcaaatcttt-tgtaggctataaaattcaaatcctgtcatttgcag

upper sequence: LOC_Os11g01270.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G003033_T01 (Zea mays), 5'ss of exon 4
CTTCGCTTTCATTTCCAGATCTCATATCAACACTTCCACAAATTGGGCTCCGAGGACTTTATCGGGGTTCTATCCCCGCAATTCTTGGTCAGTTTTCAAGgttagtgtcaattcagagttttagaggcaaatttgaatgtaggctgcaaatt-cacatcctgccatttgcag
|| | || |||||||| || ||||| ||||  ||||||||||||||||| |||||| | ||||| ||||||||||| |||||||| || |||||||||||||  |||  | |||| || |||| | |||| |||   ||||||||  ||||| || ||| || |||||||||
CTACACTCTCATTTCCTGAGCTCATTTCAAAGCTTCCACAAATTGGGCTTCGAGGATTGTATCGAGGTTCTATCCCAGCAATTCTCGGCCAGTTTTCAAGgtatgtggtatttcataggtttatatgcaa-tttttttgtaggctataaatttcaaatcttgtcatttgcag

upper sequence: LOC_Os11g01270.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA20G31800.1 (Glycine max), 5'ss of exon 5
CTTCGCTTTCATTTCCAGATCTCATATCAACACTTCCACAAATTGGGCTCCGAGGACTTTATCGGGGTTCTATCCCCGCAATTCTTGGTCAGTTTTCAAGgttagtgtcaattcagagttttag-aggcaaatttgaatgtaggctgcaaattcacatcctgccatttgcag-------------------------------------------------------------------------------------------------------------
|  |  | || || || ||  | || || |  || ||| | |||||    || ||  | ||  |||| |||||||| ||||||||||| ||||||||||||||   ||  |||     |||||  |      |||  || |   || |    ||| || |    || |  |                                                                                                              
CAACAATGTCCTTCCCTGAAATAATTTCTAAGCTGCCAGAGATTGGAAGGCGGGGTTTATACAGGGGCTCTATCCCTGCAATTCTTGGACAGTTTTCAAGgtt---gttcatttgatcttttattattttttttttcattt---cttccctctcatattcctttatcttgaaacaaataagcagaaaagtatttggtgttttaagcttctctagtaccttcccttagcaatcatataatagttattttcctttcaagctcatgctacctttgataatgcag

upper sequence: LOC_Os11g01270.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv13s0019g03870.t01 (Vitis vinifera), 5'ss of exon 4
CTTCGCTTTCATTTCCAGATCTCATATCAACACTTCCACAAATTGGGCTCCGAGGACTTTATCGGGGTTCTATCCCCGCAATTCTTGGTCAGTTTTCAAGgtta-gtgtcaattc---agagttttag---------aggcaaatttgaatgtaggctgcaaattcacatcctgccatttgcag----------------
|  | || ||||| |||||  ||||  |||  |||||| |||||||   |   ||| | ||| |||||||| |||| ||||||||||| |||||||| ||||||  ||| ||||    |    ||| |         ||   | ||  ||  |    |  |||   | |     | ||  |  |                
CAACACTCTCATTCCCAGAAATCATTGCAAAGCTTCCAGAAATTGGCGCCAAGGGATTATATAGGGGTTCTGTCCCTGCAATTCTTGGACAGTTTTCGAGgttatatgtgaatttcttactccttttgcttgtacttagttgagttgcaagatgaagtaaaaaaggaaagtaaacaataggttgcatttctttcctactg

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|58585853|gb|CF984161.1|CF984161
EST:     CGAGGACTTTATCGGGGTTCTATCCCCGCAATTCTTGGTCAGTTTTCAAG                         CCATGGTTTGAGAACAGGAATATTTGAGGCAAGCAAGCTTGTGTTAAAAAG
genomic: CGAGGACTTTATCGGGGTTCTATCCCCGCAATTCTTGGTCAGTTTTCAAGgttagtgtca ... ccatttgcagCCATGGTTTGAGAACAGGAATATTTGAGGCAAGCAAGCTTGTGTTAAAAAG




















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), 75 (downstream exon)
Score: 7

CTTCGCTTTCATTTCCAGATCTCATATCAACACTTCCACAAATTGGGCTCCGAGGACTTTATCGGGGTTCTATCCCCGCAATTCTTGGTCAGTTTTCAAGgttagtgtca ... ccatttgcagCCATGGTTTGAGAACAGGAATATTTGAGGCAAGCAAGCTTGTGTTAAAAAGTGTTGCTCCAACACTTCCAGATATTCAG




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