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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccttatcacatatttaacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT

Basic information

species Oryza sativa
transcript LOC_Os01g43150.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 10
-----gtaaccttatcacat-atttaacagtccatcacacagaggactttatgtaaattgtgttttctattgatttt-------gcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
     |  |   |||||  | ||  || || |||    ||  || ||||||| | | |  || || | |||||| ||        ||||||||||||||||||||||| |||||||||||||| ||||||||||| ||||| ||||||||||||||||| |||||||||
gcaatgctagtctatcatgtgatcgaatagaccaatgtactcagaactttatctgactcttgcttccaattgatcttttatctcacagGGAATAATTGTGATGGCTGCAACAAACTTGCCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 10
----gtaaccttatcacat-atttaacagtccatcacacagaggactttatgtaaattgtgttttctattgatttt-------gcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
    |  |   |||||||| ||  || ||  ||  | |   || ||||||  | | |  || || | |||||| ||        ||||||||||||||||||||||| ||||||||| |||| ||||||||||| ||||| ||||||||||||||||| |||||||||
gtatgctagtctatcacattatcaaatagagcaatatattcagaactttacctgactcttgcttccaattgatcttttatcttacagGGAATAATTGTGATGGCTGCAACAAACTTGGCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 2
gtaaccttatcacatatttaacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
||| | ||   |||  ||  |  |    ||   |    |  ||||   ||||||  |  |   || || ||| ||||||||||  |||||||||| ||||||||||| ||||||||||| |||||  | || || ||||| ||||| ||| |||||
gtatctttga-acagtttggagtgcaattcgttcctctggttttag--aaattgattcattattttatcttgtagGGAATAATATTGATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACTAGGCCTGGAAGATTTGATCGGCAT

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 10
gtaaccttatcacatatttaacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
||| | ||   |||  ||  |  |    |    |    |  ||||   ||||||  |  |   || || ||  ||||||||||  | |||||||| ||||||||||| ||||||||||| |||||  | || || ||||| ||||| ||| |||||
gtatctttga-acagcttggagtgcaatttgttcctctggttttag--aaattgattcattattttatcttctagGGAATAATATTAATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACGAGGCCTGGCAGATTTGATCGGCAT

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 10
-------gtaaccttatcacatatttaacagtccatcacacagaggact-ttatgtaaattgtgttttctattgattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
         ||  ||   |||| | | |  ||  |            || ||   ||| || |      | || || ||| |||||||||| || || ||||| |||||| |||| |||||||||||||| ||  | ||||| ||||||||||| ||||| |||
gtatatttcaagttttaaacatttgtgagtgtttaattagtttctctctgtttcctaatttattcaacatctttatcttgtagGGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCTTTAACAAGGCCTGGTAGATTTGATAGACAT

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 10
-----------------gtaaccttatcacatatttaacagtccatcacacagaggactttatgtaaattgtgttttctatt--gattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
                 |||   | |||   |  ||| |   |  |       |||| | ||     | | || ||||||||  | || ||||||||||||| || |||||||| ||||||||||| ||||| ||||||||||| || |||||||| |||||||| ||||| |||
gtacttgttgattaggagtagtgt-atcttgtgatta-cttccgctagtttgcaggaatataatagtactttgctttctattttggttatgcagGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACAT

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 10
gtaaccttatcacatattt-----aacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
||||| |    ||| | ||     |  |||  ||        | | ||| | ||| |||  |  |  |||  | ||| |||| |||||  ||||||| || ||||||||||| |||||||||||||||||  | ||||||||||||||||| || ||||||
gtaacatatggacaaacttgtgttattagtgaatatttttctgcatttt-tttaacttggataat--atttttcttgtagGGCATAATATTGATGGCAGCAACAAACTTGCCTGATATTCTTGATCCAGCTTTAACAAGACCTGGTAGATTTGACAGGCAT

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|25799041|gb|CA755002.1|CA755002
EST:     AAACATTGCATCAACTTCTNGTCGAGATGGATGGTTNTGAACAAAATGAG                         GGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA
genomic: AAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaaccttat ... gattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA
EST: gi|88369682|gb|CI582877.1|CI582877
EST:     GGTTTTGAACAAAATGAG                         GGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA
genomic: GGTTTTGAACAAAATGAGgtaaccttat ... gattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA
EST: gi|51946127|gb|CV152468.1|CV152468
EST:     CTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAG                         GGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA
genomic: CTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaaccttat ... gattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
                                         tattgat  putative branch site (score: 3)
                                    ttttctattgatttt  TA-rich tract