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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGGGCAGGGTTTACACACAAAGGTAGCCCAAGTTGCGGCTTCATCATTCAATATCCCTCTTAGCTCTATATTTATCTCAGAAACAAGCACTGATAAGgtgagttttggcatatggacttgctacatttgatttgcatggtctatcaatgtattcaatgaagatgttattcttatatgttactactttatttccaatgatgggttaatcagtaatcacacatgtgctcatctcaatacttag

Basic information

species Oryza sativa
transcript LOC_Os03g31550.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g31550.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G050984_T01 (Zea mays), 5'ss of exon 6
AATGGGGCAGGGTTTACACACAAAGGTAGCCCAAGTTGCGGCTTCATCATTCAATATCCCTCTTAGCTCTATATTTATCTCAGAAACAAGCACTGATAAGgtgagttttggcatatggacttgctacatttgatttgcatggtctatcaatgtattcaatgaagatgttattcttatatgttactactttatttccaatgatgggttaat-cagtaatcacacatgtgctcatctcaatacttag
 ||||| |||||||| ||||||||||||||||||||||| || || |||||||||||||||||||||||| ||||||| ||||| ||||| |||||||||||||| |  | || |||||  | |  | | ||     |||| | | |      | |   ||       || | || |   |||||  |||||||  || | || |  ||| || | |    |   |    |||||      ||||
GATGGGACAGGGTTTGCACACAAAGGTAGCCCAAGTTGCTGCCTCGTCATTCAATATCCCTCTTAGCTCTGTATTTATATCAGAGACAAGTACTGATAAGgtgaggtccgacacatggatgtaccccttctg-----catgattttt----acactagttg-------tactttttttcattact--tttatttataa-gttgtgccaatacaatgaggtgatgggattccatct----gtttag

upper sequence: LOC_Os03g31550.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA13G41520.1 (Glycine max), 5'ss of exon 11
AATGGGGCAGGGTTTACACACAAAGGTAGCCCAAGTTGCGGCTTCATCATTCAATATCCCTCTTAGCTCTATATTTATCTCAGAAACAAGCACTGATAAGgtgagttttggcatatggacttgctacatttgatttgcatggtctatcaatgtattcaatgaagatgttattcttatatgttactactttatttccaatgatgggttaatcagtaatcacacatgtgctcatctcaatacttag
||||||||| ||||| || || || || |||||| |||| |||||| | ||| ||||||||||||| ||| | ||||| ||||| || || ||||| |||||    ||| |    |  ||||  |||    | |||   | || |       |||||   |||    ||| ||| |  | |  |  |   | || | |   |   | | | | | || |                         
AATGGGGCAAGGTTTGCATACCAAAGTTGCCCAAATTGCTGCTTCAGCTTTCCATATCCCTCTTAGTTCTGTCTTTATATCAGATACTAGTACTGACAAGgta---tttagt---tacactttttacg---ggtttatgttgtttt------tattcttggaaa---ttagtctcagctatatcatccaaacttacca-agtaaataagtaatttatta-------------------------
















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|58682426|gb|CK071113.1|CK071113
EST:     TCAATATCCCTCTTAGCTCTGTATTTATCTCAGAAACAAGCACTGATAAG                         GTACCAAATGCAACACCAACAGCAGCCTCTGCTAGTTCAGATTTATATGGT
genomic: TCAATATCCCTCTTAGCTCTATATTTATCTCAGAAACAAGCACTGATAAGgtgagttttg ... caatacttagGTACCAAATGCAACACCAACAGCAGCCTCTGCTAGTTCAGATTTATATGGT
EST: gi|218495632|gb|FG967039.1|FG967039
EST:     TCAATATCCCTCTTAGCTCTGTATTTATCTCAGAAACAAGCACTGATAAG                         GTACCAAATGCAACACCAACAGCAGCCTCTGCTAGTTCAGATTTATATGGT
genomic: TCAATATCCCTCTTAGCTCTATATTTATCTCAGAAACAAGCACTGATAAGgtgagttttg ... caatacttagGTACCAAATGCAACACCAACAGCAGCCTCTGCTAGTTCAGATTTATATGGT
EST: gi|29675056|gb|CB671331.1|CB671331
EST:     TCAATATCCCTCTTAGCTCTATATTTATCTCAGAAACAAGCACTGATAAG                         GTACCAAATGCAACACCAACAGCAGCCTCTGCTAGTTCAGATTTATATGGT
genomic: TCAATATCCCTCTTAGCTCTATATTTATCTCAGAAACAAGCACTGATAAGgtgagttttg ... caatacttagGTACCAAATGCAACACCAACAGCAGCCTCTGCTAGTTCAGATTTATATGGT

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: 73 (upstream exon), 75 (downstream exon)
Score: 45

AATGGGGCAGGGTTTACACACAAAGGTAGCCCAAGTTGCGGCTTCATCATTCAATATCCCTCTTAGCTCTATATTTATCTCAGAAACAAGCACTGATAAGgtgagttttg ... caatacttagGTACCAAATGCAACACCAACAGCAGCCTCTGCTAGTTCAGATTTATATGGTGCTGCAGTTTTGGATGCTTGTCAGCAAATTATGGCTCGGATGGAACCTG




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