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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttagtacatttttgcagcttgtttcaaccactttcttttgcaaactgcttttgagttgaagtctcatgtcagAGAAATGGAGGAGATATCTGCATTTGTGAAGGATGCAATTTGCAATGATCAATGTCTAGGACGCTGCCTTTATATTCATGGTGTACCAGGCACTGGCAAG

Basic information

species Oryza sativa
transcript LOC_Os06g08790.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g08790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G455243_T01 (Zea mays), 3'ss of exon 5
gtatgttagtacatttttgcagcttgtttcaaccactttcttttgcaaactgcttttgagttgaagtctcatgtcagAGAAATGGAGGAGATATCTGCATTTGTGAAGGATGCAATTTGCAATGATCAATGTCTAGGACGCTGCCTTTATATTCATGGTGTACCAGGCACTGGCAAG
||||||   | ||| ||  | |  |||||    | | | |||    ||||||||  | || | |||| | || ||||||||||||||||||||||   |||||| ||||||||||| |||||||| || || |||||||| ||||||||||| ||||||||||| || |||||||||
gtatgtctattcatattc-ctgaatgtttgttgcgcgt-cttacaaaaactgctactcagctaaagtataatttcagAGAAATGGAGGAGATATCGATATTTGTAAAGGATGCAATCTGCAATGACCAGTGCCTAGGACGGTGCCTTTATATACATGGTGTACCTGGTACTGGCAAG

upper sequence: LOC_Os06g08790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G168249_T01 (Zea mays), 3'ss of exon 5
gtatgttagtacatttttgcagcttgtttcaaccactttcttttgcaaactgcttttgagttgaagtctcatgtcagAGAAATGGAGGAGATATCTGCATTTGTGAAGGATGCAATTTGCAATGATCAATGTCTAGGACGCTGCCTTTATATTCATGGTGTACCAGGCACTGGCAAG
|||||||  | ||| ||  | |  |||||       |  ||     ||||||||  | || | ||||||||| ||||||||||||| ||||||||   |||||| ||||||||||| |||||  | ||||| |||||||||||||||||||| ||||||||||| ||||||||||||
gtatgtttattcatcttc-ctgagtgttt-gttgtgtgcctcacaaaaactgctacttagctaaagtctcatatcagAGAAATGGATGAGATATCAATATTTGTAAAGGATGCAATCTGCAACAACCAATGCCTAGGACGCTGCCTTTATATACATGGTGTACCTGGCACTGGCAAG

upper sequence: LOC_Os06g08790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G41490.1 (Glycine max), 3'ss of exon 5
gtatgttagtacatttttgcagcttgtttcaaccactttct-----tttgcaaactgcttttgagttgaagtctcatgt---cagAGAAATGGAGGAGATATCTGCATTTGTGAAGGATGCAATTTGCAATGATCAATGTCTAGGACGCTGCCTTTATATTCATGGTGTACCAGGCACTGGCAAG
|||||||        |||| |  |  ||| ||  | ||| |     | |   ||||  |  | |    || |  | | |    |||||||||||||||||| || ||||  | || | ||| ||||  |||||||||||||| || || ||||| || ||||||||||| || || |||||||||
gtatgttgaag----tttgaacatgattttaaatattttgtatatctctctgaacttttaataatcaaaacttgcttttatttagAGAAATGGAGGAGATAACTACATTCATCAAAGGTGCTATTTCTAATGATCAATGTCTGGGGCGTTGCCTCTACATTCATGGTGTTCCGGGAACTGGCAAG

upper sequence: LOC_Os06g08790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G03900.1 (Glycine max), 3'ss of exon 7
gtatgttagtacatttttgcagcttgtttcaaccactttct-------tttgcaaactgcttttgagttgaagtctcatgtcagAGAAATGGAGGAGATATCTGCATTTGTGAAGGATGCAATTTGCAATGATCAATGTCTAGGACGCTGCCTTTATATTCATGGTGTACCAGGCACTGGCAAG
|||||||        |||| |  |  ||| ||  | ||| |       | || |   |  |  | |    | |  |    | |||||||||||||||||| |||||||  | || | |||  |||   |  |||||||||| ||||| ||||| || ||||||||||| || || |||||||||
gtatgttgaag----tttgaaaatgattttaaatattttgtatatctctctgaagtttaataatcaaaacatgcttttatttagAGAAATGGAGGAGATAACTGCATTCATCAATGGTGCTCTTTCTGACAATCAATGTCTGGGACGTTGCCTCTACATTCATGGTGTTCCGGGAACTGGCAAG

upper sequence: LOC_Os06g08790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0004g02050.t01 (Vitis vinifera), 3'ss of exon 6
gtatgttagtacatttttgcagcttgtttcaaccactttcttttgcaaactgcttttgagttgaag--------tctcatgtcagAGAAATGGAGGAGATATCTGCATTTGTGAAGGATGCAATTTGCAATGATCAATGTCTAGGACGCTGCCTTTATATTCATGGTGTACCAGGCACTGGCAAG
|||||| ||       ||| |  || | |      | || ||||||  |||  |||  | | || |        | | |||| || |||||||| |||||| |||||||| | || | ||| || ||||||||||||||| | ||||| ||||| || ||||||||||| || || |||||||||
gtatgtgaga-----cttg-aatttttataggttccatttttttgcgcactagtttctaatagaggacatgggcttttatgt-agGGAAATGGAAGAGATAACTGCATTTATAAAAGGTGCCATCTGCAATGATCAATGTTTGGGACGTTGCCTGTACATTCATGGTGTTCCTGGAACTGGCAAG

upper sequence: LOC_Os06g08790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0004g00530.t01 (Vitis vinifera), 3'ss of exon 5
gtatgttag---tacatttttgcagcttgtttcaaccactttcttttgcaaactgcttttgagttgaag--------tctcatgtcagAGAAATGGAGGAGATATCTGCATTTGTGAAGGATGCAATTTGCAATGATCAATGTCTAGGACGCTGCCTTTATATTCATGGTGTACCAGGCACTGGCAAG
|||||| ||   |  ||||||  ||   ||| ||      || ||||||  |||  |||  | | || |        | | |||| || |||||||| |||||| |||||||| | || | ||| || ||||||||||||||||| ||||| ||||| || ||||||||||| || || |||||||||
gtatgtgagacctgaatttttatag---gttcca------tttttttgcgcactagtttctaatagaggacatgggcttttatgt-agGGAAATGGAAGAGATAACTGCATTTATAAAAGGTGCCATCTGCAATGATCAATGTCTGGGACGTTGCCTGTACATTCATGGTGTTCCTGGAACTGGCAAG

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|58680494|gb|CK069181.1|CK069181
EST:     GCAACCCTGTTATTGGCAACTCTTCCTAAGTCGTTACCTTGTAGGGATAA                         AGAAATGGAGGAGATATCTGCATTTGTGAAGGATGCAATTTGCAATGATCA
genomic: GCAACCCTGTTATTGGCAACTCTTCCTAAGTCGTTACCTTGTAGGGATAAgtatgttagt ... ctcatgtcagAGAAATGGAGGAGATATCTGCATTTGTGAAGGATGCAATTTGCAATGATCA




















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: 55 (upstream exon), 50 (downstream exon)
Score: 3

TTCCTGAACATGTCCGGTGTCATCAAAAGACCAATCTGGAGAAGGCAAAAGCAACCCTGTTATTGGCAACTCTTCCTAAGTCGTTACCTTGTAGGGATAAgtatgttagt ... ctcatgtcagAGAAATGGAGGAGATATCTGCATTTGTGAAGGATGCAATTTGCAATGATCAATGTCTAGGACGCTGCCTTTATATTCATGGTGTACCAGGCACTGGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtttcaaccactttcttttgcaaactgcttttgagttgaagtctcatgtcagAGAAATGGAGGAGATATCTGCATTTGTGAAGGATGCAATTTGCAATGATCAATGTCTAGGACGCTGCCTTTATATTCATGGTGTACCAGGCACTGGCAAG
              tttctttt  TA-rich tract