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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGGGATATTAACATGAACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAGgtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcag

Basic information

species Oryza sativa
transcript LOC_Os01g41630.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 10
CTTTGGGATATTAACATGAACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAGgtaattctgtacatgttaaga-tgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcag
||||||||| |||| ||||| || ||||||||||||||||||||||||||||||||| ||||||| |||||||||   | |||||||||| | ||||||  ||  ||||||| |||  ||| | || | |   |||  ||||||  |  ||||| ||||| || |||   | ||||||||
CTTTGGGATGTTAAGATGAATTCCGGTCCAGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttcttccatgttaagagtaaataattgatgattctttgtggacaatgcataacacatatttttgctggagccaaactgatccatgtgttactt---ggaactgcag

upper sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 10
CTTTGGGATATTAACATGAACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAGgtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcag
||||||||| |||| ||||| |||||||| ||||||||||||||||||||||||||| ||||||| |||||||||   | ||||||||||| ||||||  ||  ||||||| | |  ||||| |  | |   |||  |||||  ||  ||||| ||||| || ||     |||||||||
CTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactc---aaaactgcag

upper sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 10
CTTTGGGATATTAACATGAACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAGgtaattctgtacatgttaag--atgaataa-tccatacttctttga--ggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcag
 | ||||| ||||| ||| | || || || |||||||| |||||||||||||||||||| || ||||||||   |   ||  || | |   ||||||   |   ||||  ||||   |  | || |    | |    |||   | ||      | |                            
TTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTGAGACCCAAGgt---ttgataagtgatgaattatgaatttctttctactgttttgtctgagttataactggttatgctttttgtttgaacgtgccag----------------------------

upper sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 10
CTTTGGGATATTAACATGAACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAGgtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcag
 | ||||| || || ||| | ||||||||||||||||||||||||||||| |||||||||||||| ||||| |   |   |||||| | || | ||||    | |       | ||         |  |  |  |||    |||||||  |  |||| | ||  |  |           
TTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACATTCCAGGTTCACGAGTATTTAAGGCCAAAGgttagatt-cccatgtttatataagtaatgagcaat-------gaattcctgctgctttatcaagtcat---agtaact--ggctcatttttttttggccag--------

upper sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 10
CTTTGGGATATTAACATGAACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAGgtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcag
 | ||||| ||||| ||| | || || || |||||||| ||||||||||||||||||||||| |||||||| |   |     |||| |||| | | ||  ||     | |||   ||||      |  |||  ||    |   ||   ||| || || | ||   |    | |   |||
TTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAGgttagatt-cctgtgtttagataagtgatgaat-----tatgaatttcat------tctactgctttgtcgagttataactggtt-atattttatgtttgaacatgccag

upper sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 10
CTTTGGGATATTAACATGAACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAGgtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcag
 | ||||| || || ||| | ||||||||||||||||| |||||||||||||||||||||||||| ||||| |   |   ||||||  |||||  |||  ||   |  |     |||| |    |  ||||   ||  |    |   | ||                            
TTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTAAGGCCAAAGgttagatt-cccatgtttggatgagcaatgaatttctgctgctttatcaagttatagtaactggctcttt----tttttttggccag-----------------------

upper sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 10
CTTTGGGATATTAACATGAACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAGgtaattctgtacatgtta-agatgaataatccatacttctttgaggatcatgaacaataaacta-tttcactggagtaactctgattcatgtattgcttcctgaaactgcag
 | ||||| ||||| ||| |||| || |||||| |||| |||||||||||||| |||||||| || ||||| |   ||      | | | | |  | |  || |     ||    || |    |   |  ||| ||| ||        ||||| ||| |   ||   ||| |         
TTATGGGACATTAATATGGACTCAGGCCCAGTTTCAACCTTCCAGGTTCATGAATATTTAAGACCTAAGgtgagcttgctttcctcagaaaagtcttacacagaacaacttctacattactctctgcatgctaattttacc-------ctctgtttctttccttctctccag---------

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|38568585|gb|CD670800.1|CD670800
EST:     ACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAG                         CTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGT
genomic: ACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAGgtaattctgt ... gaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGT
EST: gi|58590817|gb|CF989125.1|CF989125
EST:     ACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAG                         CTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGT
genomic: ACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAGgtaattctgt ... gaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGT

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: 49 (upstream exon), 72 (downstream exon)
Score: 12

CTTTGGGATATTAACATGAACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAGgtaattctgt ... gaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG




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