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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAGgtcaatcattcactattctcacttaaatttatatgtttgatttcagaatgtgccttttcctttgtttttaagcagattatttggttctgcacacttagaa...

Basic information

species Oryza sativa
transcript LOC_Os08g42410.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G043198_T03 (Zea mays), 5'ss of exon 6
GCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAGgtcaatcattcact--attct-cacttaaatttatatgtttgatt-tcagaatgtgccttttcctttgtttttaagcagattatttggttctgcacacttagaa
   || || ||||| |||||||||||||| || || || |||||||| ||| | || |||||||||||||||||||| || ||||||||||    ||   |  ||||| ||  | |   ||    ||  ||| | | ||| |    || | ||  ||| |       | ||| |  | |   | ||| |  
---GGCTTCACTGGCATTGGTGTTGGTGCCGCTTACCATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtttgatcaattctgcaaatcaccatactaattcaattattacaatatttgcttgctttgatttgttctttactcattggcatat---ctcttggt-

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G043198_T02 (Zea mays), 5'ss of exon 6
GCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAGgtcaatcattcact--attct-cacttaaatttatatgtttgatt-tcagaatgtgccttttcctttgtttttaagcagattatttggttctgcacacttagaa
|| || || ||||| |||||||||||||| || || || |||||||| ||| | || |||||||||||||||||||| || ||||||||||    ||   |  ||||| ||  | |   ||    ||  ||| | | ||| |    || | ||  ||| |       | ||| |  | |   | ||| |  
GCGGGCTTCACTGGCATTGGTGTTGGTGCCGCTTACCATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtttgatcaattctgcaaatcaccatactaattcaattattacaatatttgcttgctttgatttgttctttactcattggcatat---ctcttggt-

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA14G02380.2 (Glycine max), 5'ss of exon 6
GCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAGgtc--aatcattcactattctcacttaaatttatatgtttgatttcagaatgtgccttttcctttgtttttaagcagattatttggttc-tgcacacttagaa
||||| ||| |||| ||||| ||||||||||| ||  | |||||  | ||||| || ||||| ||||| ||||||||||| ||||||||   | |   ||   |||    | |   ||| |    |||| |   |||  ||  |  |   || |||  |      | | ||  ||  || | |  ||   
GCTGGGTTTGCTGGGATTGGAGTTGGTGCTGCTTACTATGGTCTAAGGCCTGTTGTGGAGTTTATGACTTTTAACTTCTCCATGCAGgttggagtttatcttgattgcatcctttctttcttaaattgagtgt-gaacttgagtgatatattttttacagcagcgtcacttaatttatgtatatgtac--

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 6
GCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAGgtc--aatcattcactatt-ctcacttaaatttatatgtttgatttcagaat--gtgccttttcctttgtttttaagcagattatttggttctgcacacttagaa
||||| |||||||| ||||| ||||| ||||| ||  | |||||  | ||||| || ||||||||||| ||||||||||| ||||||||   | |   ||   ||| |   |||   ||  ||  ||   | |||   |  |||   | || |||  |  |  ||   |||  |   | || | |  ||   
GCTGGGTTTACTGGGATTGGAGTTGGCGCTGCTTACTATGGTCTAAGGCCTGTTGTGGAGTTCATGACTTTTAACTTCTCCATGCAGgttggagtttatcttgattgcatcctttctttcttaaattgagtgtcaagttaagtgatatgtcttttactgctgcgccacttaact---tatgtatatgtac--

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 7
GCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAGgtcaatcattcactattctcacttaaatttatatgtttgatttcagaatgtgccttttcctttgtttt---taagca-gattatttggttctgcacacttagaa-----
||||| |||||||||||||| |||||||||||||||   ||  |    || || || || || ||||| |||||||||||||||||||| |  | ||   | || | |        |||   ||  ||   | | | ||||| || |||||  ||   || |||  ||| ||  |||   || |    | |     
GCTGGATTTACTGGAATTGGAGTTGGTGCTGCCTATGCTGGCTTAAAGCCCGTTGTAGAATTTATGACGTTTAACTTCTCTATGCAGgttag-cgttggtttttgtta--------tattctttgaatactacattttgcctctttctttgacttgattatgcataattgttgcgttactcagatcatgcactctg

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 5'ss of exon 7
GCTGGTTTTACTGGAATTGGTGTTGGTGCTGCCTATCAAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAGgtcaatcattcactattctcacttaaatttatatgtttgatttcagaatgtgccttttcctt-tgtttttaagcagattatttggttctgcacacttagaa--
|||||||||||||| ||||| ||||||||||| ||  | ||||||   ||||| || ||||||||||||||||| |||||||||||||| |     | |  | | |    | || ||||       |||||    | ||  |||   |  |||| | ||   ||   ||| | |  |     | | ||  
GCTGGTTTTACTGGGATTGGAGTTGGTGCTGCTTACTATGGTCTTAAGCCTGTTGTAGAGTTCATGACATTTAATTTCTCTATGCAGgttagagtcttatcactatatactcaaattatgaa---aatttctagttctgattttatttgatgttctcaaattgaacctttagctgggattggtcaaaact

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|428335|gb|D24483.1|D24483
EST:     AAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAG                         GCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCT
genomic: AAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAGgtcaatcatt ... gcatattcagGCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCT
EST: gi|218484233|gb|FG953202.1|FG953202
EST:     AAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAG                         GCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCT
genomic: AAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAGgtcaatcatt ... gcatattcagGCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCT