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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAACAATTCCACTCGATGGAGATGAAGATGCAACTGAGGAGGTCTTGGATCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAGgtagagctactaatggagatagctagcacatcctcttttttgctactctgcttctactaactcttaactggatatgtgattgatggtttcag

Basic information

species Oryza sativa
transcript LOC_Os02g32730.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32730.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G040843_T02 (Zea mays), 5'ss of exon 3
CGAACAATTCCACTCGATGGAGATGAAGATGCAACTGAGGAGGTCTTGGATCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAGgtagagctactaatggagatagctagcacatcctcttttttgctactctgcttctactaactcttaactggatatgtgattgat----ggtttcag
|| ||||||||||| ||||| ||||| |||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||  | |  ||||||   | | |      |  |  |||| |||||||||| |   ||  || | |  | | ||  ||||  |     || |||||
CGGACAATTCCACTTGATGGTGATGAGGATGCAACTGAGGAGGTCTTGGATCCTGATTTTGGGGAAGCCGCAATAGGCCGTGTGGCACCTGTTGATTCAGgtaatgttgataatgggtttggttg-----tttttgttttggctactctgcattccctg-ctttaattttggtacctgataaaaactgggcttcag

upper sequence: LOC_Os02g32730.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA05G31920.1 (Glycine max), 5'ss of exon 2
CGAACAATTCCACTCGATGGAGATGAAGATGCAACTGAGGAGGTCTTGGATCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAGgtagagctactaatggagatagctagcacatcctctttttt-gct-----actctgcttctactaactcttaactggatatgtgattgatggtttcag
 | ||| ||||  | ||||| |||||   |||||| || ||||| ||||||||||| ||||| |||||||| || || ||||| || || ||||||||||||| |   | ||||  |   |      | ||  ||||   | |||     |   | |    |||  |  |  | ||   |    ||  ||| | ||||
AGGACAGTTCCTTTGGATGGTGATGATTCTGCAACAGAAGAGGTTTTGGATCCTGACTTTGGAGAGGCAGCCATTGGGCGTGTTGCTCCAGTTGATTCAGgtaaaataaataatcaaatcaatagaaatattttcttacatagctgaagaaacttaccataactctccttggattgctgaacatatatatgatctcag

upper sequence: LOC_Os02g32730.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G15220.1 (Glycine max), 5'ss of exon 3
CGAACAATTCCACTCGATGGAGATGAAGATGCAACTGAGGAGGTCTTGGATCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAGgtagagctactaatggagatagctagcacatcctcttttttgctactctgcttctacta----actcttaa-----ctggatatgtg--attgatggtttcag
 | ||| ||||  | || || |||||   |||||| || || || ||||||||||| ||||| |||||||| || || ||||| || || ||||||||||||| |   | ||||  |   |      | ||  ||||   |   |         ||| |    |||| |       ||| | || |   |    || | ||||
AGGACAGTTCCTTTGGACGGTGATGATTCTGCAACAGAAGAAGTTTTGGATCCTGACTTTGGAGAGGCAGCCATTGGTCGTGTTGCTCCAGTTGATTCAGgtaaaataaataatcaaatcaatagaaatattttcttacatagcagaagaaacttaccataatactccttgggttgctgaacatattgcacctgtgatctcag

upper sequence: LOC_Os02g32730.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv06s0061g01520.t01 (Vitis vinifera), 5'ss of exon 4
CGAACAATTCCACTCGATGGAGATGAAGATGCAACTGAGGAGGTCTTGGATCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAGgtagagctactaatggagatagctagcacatcctcttttttgc-tactctgcttctactaactcttaactggatatgtgattgat---ggtttcag--------
|| ||  ||||||| ||||| |||||   ||||||||| || || ||||||||||| ||||| ||||||||||| |||||||| ||||| |||||||| |||| |||   || |      |   |||   | ||| ||   |  |  | | ||| ||  |    |||  |  | ||     | ||    ||| | |        
CGCACTGTTCCACTTGATGGTGATGATTCTGCAACTGAAGATGTATTGGATCCTGACTTTGGTGAGGCAGCAATTGGCCGTGTTGCACCCGTTGATTCTGgta-agcagatattctgttcaataagc---ttctcattaaagtatggtttacttttatgagtatttacatttaaattcttctcattttagttgctgagaaacca

upper sequence: LOC_Os02g32730.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv13s0074g00720.t01 (Vitis vinifera), 5'ss of exon 4
CGAACAATTCCACTCGATGGAGATGAAGATGCAACTGAGGAGGTCTTGGATCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAGgtagagctac-taatggagatagct---agcacatcctctttt-------ttgctactctgcttctactaactcttaactggatatgtgattgatggtttcag
|| ||| |||| || ||||| |||||   |||||| || ||||| ||||||||||||||||| || |||||||| |||||||| ||||||||||| || |||| | | |   |   |||   | |   || | | |   |||        ||   | |     ||||  || ||| |  |     | |||| |     |||||
CGCACAGTTCCCCTGGATGGTGATGACTCTGCAACAGAAGAGGTATTGGATCCTGATTTTGGAGAAGCAGCAATTGGCCGTGTTGCACCTGTTGACTCTGgtaaatcaatacagcagagcatgttttaagaagaactaatttcacttgcattagaatttaaactctagcaaatctaagttcatgttatgat-gtcaacttcag

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|58688014|gb|CK076701.1|CK076701
EST:     TCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAG                         GTCTATGGTGGATCATATTACTTAGGGCGTATGGAAAGTGTTCAGGAGATC
genomic: TCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAGgtagagctac ... atggtttcagGTCTATGGTGGATCATATTACTTAGGGCGTATGGAAAGTGTTCAGGAGATC
EST: gi|58695712|gb|CK084399.1|CK084399
EST:     TCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAG                         GTCTATGGTGGA
genomic: TCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAGgtagagctac ... atggtttcagGTCTATGGTGGA
EST: gi|29682293|gb|CB678568.1|CB678568
EST:     TCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAG                         GTCTATGGTGGATCATATTACTTAGGGCGTATGGAAAGTGTTCAGGAGATC
genomic: TCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAGgtagagctac ... atggtttcagGTCTATGGTGGATCATATTACTTAGGGCGTATGGAAAGTGTTCAGGAGATC
EST: gi|29627287|gb|CB632298.1|CB632298
EST:     TCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAG                         GTCTATGGTGGATCATATTACTTAGGGCGTATGGAAAGTGTTCAGGAGATC
genomic: TCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAGgtagagctac ... atggtttcagGTCTATGGTGGATCATATTACTTAGGGCGTATGGAAAGTGTTCAGGAGATC
EST: gi|29629284|gb|CB634295.1|CB634295
EST:     TCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAG                         GTCTATGGTGGATCATATTACTTANGGCGTATGGAAAGTGTTCAGGAGATC
genomic: TCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAGgtagagctac ... atggtttcagGTCTATGGTGGATCATATTACTTAGGGCGTATGGAAAGTGTTCAGGAGATC

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), 73 (downstream exon)
Score: 35

CGAACAATTCCACTCGATGGAGATGAAGATGCAACTGAGGAGGTCTTGGATCCTGATTTTGGGGAGGCAGCAATAGGCCGTGTGGCACCTGTTGATTCAGgtagagctac ... atggtttcagGTCTATGGTGGATCATATTACTTAGGGCGTATGGAAAGTGTTCAGGAGATCTGACAGTTCAGGAGAGAATTGATGTTCAGACTGGAATTAAAATGATATT




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