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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacatttcttgtctgctttgcaattctgtactctgtacaatttctggattcaacaaagtggctcacttctttgcatattgacagGTACAGTATGGTTTTGGCTGATAATGTTGATGGTGGAGATGACCTCGATCTTATTGTTACTACCATGAATGGCAATGTCTTCTGCTTCTCCACTCCCTCT

Basic information

species Oryza sativa
transcript LOC_Os03g61050.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g61050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G479744_T01 (Zea mays), 3'ss of exon 6
gtatgacatttcttgtctgctttgcaa----ttctgtactctgtacaatttctggattca--------acaaagtgg-ctcacttctttgcat--attgacagGTACAGTATGGTTTTGGCTGATAATGTTGATGGTGGAGATGACCTCGATCTTATTGTTACTACCATGAATGGCAATGTCTTCTGCTTCTCCACTCCCTCT
||||| | | |||| | |||||| | |    ||   ||   |          ||| | ||        | ||||||| || | |  |   | |  | || |||||||| |||||||||||||||||| || ||||||||||||||||| |||||||||||||| || ||||||||||| |||||||||||||||||||  || 
gtatgccttatcttctttgcttttctagatgtttgatatcattgctggggattgggtacatcatttccataaagtgggctgattgttgcactttgactgtcagGTACACTATGGTTTTGGCTGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCA

upper sequence: LOC_Os03g61050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G105976_T01 (Zea mays), 3'ss of exon 2
gtatgacatttcttgtctgctttgcaa---ttctgtactctgtacaatttctggatt-----caacaaagtg-gctcacttctttgcat----attgacagGTACAGTATGGTTTTGGCTGATAATGTTGATGGTGGAGATGACCTCGATCTTATTGTTACTACCATGAATGGCAATGTCTTCTGCTTCTCCACTCCCTCT
 ||||  |||| || |||||| ||| |   ||  |||   | |     | ||| | |     ||| |||||| |||||||||||||||     | |||||||||||  |||||||||||||| ||||| ||||| ||||| || || ||||||||||||||||| ||||| ||||| |||||  |||| ||||||||||| 
-tatgcaatttattctctgctctgcgagattttggtagcatttttgggtactgtacttacatcaataaagtgcgctcacttctttgcactttgactgacagGTACACCATGGTTTTGGCTGACAATGTGGATGGCGGAGACGATCTTGATCTTATTGTTACTACTATGAACGGCAACGTCTTTAGCTTTTCCACTCCCTCA

upper sequence: LOC_Os03g61050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA01G27250.2 (Glycine max), 3'ss of exon 10
gtatgacatttcttg-tctgctttgcaattctgtactctgtacaa-tttctggattcaacaaagtggctcacttctttgcatattgacagGTACAGTATGGTTTTGGCTGATAATGTTGATGGTGGAGATGACCTCGATCTTATTGTTACTACCATGAATGGCAATGTCTTCTGCTTCTCCACTCCCTCT
||| || |||  ||   |||  |    | | ||   ||||| | | ||||| ||   |   | ||| |   |||  |         |||| || || ||||| ||||| || || ||||||||||| ||||| || ||||| ||||| || || |||||||||||||||||||||||||| || || |||
gtaagagattctttaacctgtctcttgaatatgctttctgtcctactttcttga---agttatgtgccattctttct---------acagTTATAGCATGGTCTTGGCAGACAACGTTGATGGTGGGGATGATCTTGATCTAATTGTCACAACTATGAATGGCAATGTCTTCTGCTTCTCAACCCCGTCT

upper sequence: LOC_Os03g61050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA03G14690.1 (Glycine max), 3'ss of exon 12
gtatgacatttcttgtctgctttgcaattctgtactctgtacaatttctggattcaacaaagtggctcacttctttgcatattgacagGTACAGTATGGTTTTGGCTGATAATGTTGATGGTGGAGATGACCTCGATCTTATTGTTACTACCATGAATGGCAATGTCTTCTGCTTCTCCACTCCCTCT
||| || |||  ||  ||| | |     |||    | ||     | |     ||     ||||      |   |||     || ||||||| || ||||| ||||| || |||||||||||||| ||||| || ||||| ||||| || || |||||||||||||||||||||||||| || || |||
gtaagagattctttaactgttat----ctctcggatatgctttctgttctactttcttgaagttatgtgccattttt----tttacagGTATAGCATGGTCTTGGCAGACAATGTTGATGGTGGGGATGATCTTGATCTAATTGTCACAACAATGAATGGCAATGTCTTCTGCTTCTCAACCCCATCT

upper sequence: LOC_Os03g61050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT3G09090.2 (Arabidopsis thaliana), 3'ss of exon 10
gtatgacatttcttgtctgctttgcaattctgtactctgtacaatttctggattcaacaaagtggctcacttctttgcatattgacagGTACAGTATGGTTTTGGCTGATAATGTTGATGGTGGAGATGACCTCGATCTTATTGTTACTACCATGAATGGCAATGTCTTCTGCTTCTCCACTCCCTCT
||| | || || |||  | || | |    | ||| | | |  | | | | ||  || ||| ||   ||            | | |||| ||||| ||||| ||||||||||||||||| ||||||||||| ||||||||||||||  | || |||||||| || ||||| |||||||| || || |||
gtaagtcactt-ttgcttcctct-cggcac-gtaatatctttagtattttgac-caccaatgtctttcg-----------agttacagATACAGCATGGTCTTGGCTGATAATGTTGACGGTGGAGATGATCTCGATCTTATTGTCTCAACTATGAATGGAAACGTCTTTTGCTTCTCAACGCCTTCT

upper sequence: LOC_Os03g61050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv08s0007g01790.t01 (Vitis vinifera), 3'ss of exon 10
gtatgacatttcttgtctgctttgca-attctgtact-ctgtacaatttct--ggattcaacaaagtggctcacttctttgcatattgacagGTACAGTATGGTTTTGGCTGATAATGTTGATGGTGGAGATGACCTCGATCTTATTGTTACTACCATGAATGGCAATGTCTTCTGCTTCTCCACTCCCTCT
||| |  ||  ||   || || | ||  ||  ||  | ||||  ||||| |    |||     ||       |   ||||      | |||| || || |||||  |||| || |||||||||||||||||||| || |||||||||||||| ||||||||||||||||| || ||||| || |||||  ||
gtaagttatc-ctccactactattcatgtttagttttactgtttaatttttcaaaatttgtttaaaatataaatgccttta-----ttacagATATAGCATGGTCCTGGCGGACAATGTTGATGGTGGAGATGATCTTGATCTTATTGTTACAACCATGAATGGCAATGTATTTTGCTTTTCAACTCCTGCT

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|66922723|gb|CX109571.1|CX109571
EST:     GGGCTCAAGTGGCTGTGCAGATGTTGTTGACATTGGAGAGACCTC                         GTACAGTATGGTTTTGGCTGATAATGTTGATGGTGGAGATGACCTCGATCT
genomic: GGGCTCAAGTGGCTGTGCAGATGTTGTTGACATTGGAGAGACCTCgtatgacatt ... atattgacagGTACAGTATGGTTTTGGCTGATAATGTTGATGGTGGAGATGACCTCGATCT




















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: 75 (upstream exon), 73 (downstream exon)
Score: 20

CTAAAGGCCTCACCCTTGCTACTACATCCTTTGATGGTTACTTGTATTTGATTGAGGGCTCAAGTGGCTGTGCAGATGTTGTTGACATTGGAGAGACCTCgtatgacatt ... atattgacagGTACAGTATGGTTTTGGCTGATAATGTTGATGGTGGAGATGACCTCGATCTTATTGTTACTACCATGAATGGCAATGTCTTCTGCTTCTCCACTCCCTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actctgtacaatttctggattcaacaaagtggctcacttctttgcatattgacagGTACAGTATGGTTTTGGCTGATAATGTTGATGGTGGAGATGACCTCGATCTTATTGTTACTACCATGAATGGCAATGTCTTCTGCTTCTCCACTCCCTCT
                              ggctcac  putative branch site (score: 20)
      tacaattt  TA-rich tract