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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGATTCACGCAGAACCAGCTGACATTGTGGAAGTACCCGTCGATGGTTAAGATGGCTGAACTCACTGGCCATACTTCCCGTGTCCTTTTCATGGCTCAGgtgagtttcttcttgattagtagttttgcagtcactgcctataagttaatctgttatttgctgatcgtcttactgtgattgaactacag

Basic information

species Oryza sativa
transcript LOC_Os02g47180.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47180.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA01G43980.1 (Glycine max), 5'ss of exon 4
CGGATTCACGCAGAACCAGCTGACATTGTGGAAGTACCCGTCGATGGTTAAGATGGCTGAACTCACTGGCCATACTTCCCGTGTCCTTTTCATGGCTCAGgtgagtttcttcttgattagtagttttgcagtcac-tgcctataa-gttaatct----gttatttgctgatcgtcttactgt--gattgaactacag
 || || || ||||| ||| | ||| | ||||| ||||| || ||||| ||||||||||| |||||||| ||||| ||| | || ||||||||||| ||||| | ||  || | ||||  | |||  ||||  || ||  || |  ||  || |    | | ||| |||||      | ||    | |    | |||
TGGTTTTACCCAGAATCAGTTAACACTTTGGAAATACCCCTCAATGGTGAAGATGGCTGAGCTCACTGGTCATACCTCCAGAGTTCTTTTCATGGCCCAGgtaatttatttttggatt--ttgttgagcagaaacctgattagattgtctattttgaggcttttttctgattagtgcaatgccaaacttcctttcag

upper sequence: LOC_Os02g47180.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA11G01450.1 (Glycine max), 5'ss of exon 3
CGGATTCACGCAGAACCAGCTGACATTGTGGAAGTACCCGTCGATGGTTAAGATGGCTGAACTCACTGGCCATACTTCCCGTGTCCTTTTCATGGCTCAGgtgagtttcttcttgattagtagttttgcagtcactgcctataagttaatctgttatttgctgatcgtcttactgtgattgaactacag
 || || || ||||| ||| | ||| | ||||| ||||| || ||||| ||||||||||| |||| ||||||||||||  | || ||||||||||| ||||| | ||| |||| ||  |  |   |    |    ||  | |    | ||  |   ||| |||||     |  ||| |     || |||
TGGTTTTACCCAGAATCAGTTAACACTTTGGAAATACCCCTCAATGGTGAAGATGGCTGAGCTCAATGGCCATACTTCAAGAGTTCTTTTCATGGCCCAGgt-aattttttctcgagcacaaacctgattgat-ttgattgtcttattatgaggcttttcctgattagtgtgatgtcaacttccttcag

upper sequence: LOC_Os02g47180.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT4G33260.2 (Arabidopsis thaliana), 5'ss of exon 4
CGGATTCACGCAGAACCAGCTGACATTGTGGAAGTACCCGTCGATGGTTAAGATGGCTGAACTCACTGGCCATACTTCCCGTGTCCTTTTCATGGCTCAGgtgagtttct---tcttgattagtagttttgcagtcactgcctataagttaatctgttatttg---ctgatcgtcttactgtgattgaactacag
 || || || ||||| ||||| ||| | ||||||||||| || ||||| || |||||||| |||||||| ||||| ||  | || || |  ||||| ||||| |  |  |   | |   | ||| ||   | |||    | || | || | ||    |  ||     ||      ||  |||| ||   ||||||
TGGGTTTACACAGAATCAGCTTACACTTTGGAAGTACCCATCCATGGTGAAAATGGCTGAGCTCACTGGTCATACATCAAGAGTTCTATATATGGCCCAGgtaacgtcatcaatttctttaagtggtgaagtagtttgagtctttgaggtcattcagtccttaaacttgtgttgtttgttgtgtttt--ctacag

upper sequence: LOC_Os02g47180.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv16s0039g02510.t01 (Vitis vinifera), 5'ss of exon 4
CGGATTCACGCAGAACCAGCTGACATTGTGGAAGTACCCGTCGATGGTTAAGATGGCTGAACTCACTGGCCATACTTCCCGTGTCCTTTTCATGGCTCAGgtg--agtttc--ttcttgattagta---gttttgcagtcactg-cctataagttaatctgttatttgctgatcgtcttactgtgattgaactacag---
 || ||  | ||||| || || ||  ||||||||||||| || ||||| |||||  |||| || ||||| ||||| ||| | || |||||||||||||||||   | | |   |  | | |||||    ||||  | || ||    || || |   || | |  ||  | ||   | | |  || | || |    |    
TGGCTTTTCACAGAATCAACTTACTCTGTGGAAGTACCCATCAATGGTGAAGATTACTGAGCTTACTGGTCATACATCCAGAGTTCTTTTCATGGCTCAGgtactaatatggatcttagtttagtgaatgtttctcggtaacaaatctttatggctatgtttggttcccagaaaatttaagagtaaatgcaaagaaaaga

upper sequence: LOC_Os02g47180.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv15s0107g00320.t01 (Vitis vinifera), 5'ss of exon 4
CGGATTCACGCAGAACCAGCTGACATTGTGGAAGTACCCGTCGATGGTTAAGATGGCTGAACTCACTGGCCATACTTCCCGTGTCCTTTTCATGGCTCAGgtg--agtttc----ttcttgattagtagttttgcagtcactgcc-tataagttaatctgttatttgctgatcgtcttactgtgattgaactacag
||| || || ||||| || || ||  ||||||||||||| |||||||| || ||||| || || ||||| ||||| ||||| ||||||||||||||||||||   | | |     |||     ||     ||    || | |  | ||  ||  ||||||    || |||||  | |   |||  |       |||
CGGTTTTACACAGAATCAACTCACTCTGTGGAAGTACCCATCGATGGTGAAAATGGCAGAGCTTACTGGTCATACATCCCGAGTCCTTTTCATGGCTCAGgtactaatataaaaattcccttctatcttcttgttggtgattttcgtagtagccaatctgcgggtt-ctgatt-tttccttgttctcttttaccag

upper sequence: LOC_Os02g47180.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S27_42V6.1 (Physcomitrella patens), 5'ss of exon 8
CGGATTCACGCAGAACCAGCTGACATTGTGGAAGTACCCGTCGATGGTTAAGATGGCTGAACTCACTGGCCATACTTCCCGTGTCCTTTTCATGGCTCAGgtgagtttcttcttgattagtagttttgcagtcactg---cctataagttaatctgttatttgctgatcgtcttactgtgattgaactacag
 ||||| |  || || |||||     |||||||||| ||||| ||||| ||| ||||||| |||||||||||||| ||  | ||| |     |||| ||||| |  ||||   |  |||| || |  |  ||| ||     |     ||  |||     | || |  |    |       |||      |||
TGGATTTAGCCAAAATCAGCTATGTCTGTGGAAGTATCCGTCTATGGTGAAGCTGGCTGAGCTCACTGGCCATACCTCAAGAGTCTTGCATCTGGCACAGgtaaccttctgggtctttaggagata-gtggtctctcaattccgctggtgtatccaacctatgtttgtaacttgtgcaatattctctggcag

upper sequence: LOC_Os02g47180.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ31840 (Selaginella moellendorffii), 5'ss of exon 3
CGGATTCACGCAGAACCAGCTGACATTGTGGAAGTACCCGTCGATGGTTAAGATGGCTGAACTCACTGGCCATACTTCCCGTGTCCTTTTCATGGCTCAGgtgagtttcttcttgattagtagttttgcagtcactgcctataagttaatctgttatttgctgatcgtcttactgtgattgaactacag
 |||||||  ||||||||| |||  ||||||||||||||||| ||||| |||||||| ||||| || || || || ||| | ||| |   | |||| |||||   | |  ||||| || ||  |    |||    |  ||| |      | ||||  |||| |                          
TGGATTCAGCCAGAACCAGTTGATCTTGTGGAAGTACCCGTCTATGGTGAAGATGGCGGAACTTACCGGTCACACATCCAGAGTCTTGCACTTGGCGCAGgtagatgt--tcttgcttggtt-tccatcagctggtatcta-accacgctgtgttcgttgcag--------------------------

upper sequence: LOC_Os02g47180.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ13752 (Selaginella moellendorffii), 5'ss of exon 3
CGGATTCACGCAGAACCAGCTGACATTGTGGAAGTACCCGTCGATGGTTAAGATGGCTGAACTCACTGGCCATACTTCCCGTGTCCTTTTCATGGCTCAGgtgagtttcttcttgattagtagttttgcagtcactgcctataagttaatctgttatttgctgatcgtcttactgtgattgaactacag
||| ||||  ||||||||||| |   | |||||||||||||||||||| |||||||| || || || || || || ||  | |||||    ||||| |||||  | | | | |          || |   |  | ||| |   |  ||   |  ||||||| |                          
CGGCTTCAGCCAGAACCAGCTCATTCTCTGGAAGTACCCGTCGATGGTGAAGATGGCGGAGCTGACCGGGCACACCTCGAGGGTCCTGCATATGGCACAGgtctgctccctttct--------ttcttaggaaagtgcttgagacatacctttgtatttgcag--------------------------

upper sequence: LOC_Os02g47180.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ29191 (Selaginella moellendorffii), 5'ss of exon 3
CGGATTCACGCAGAACCAGCTGACATTGTGGAAGTACCCGTCGATGGTTAAGATGGCTGAACTCACTGGCCATACTTCCCGTGTCCTTTTCATGGCTCAGgtgagtttcttcttgattagtagttttgcagtcac-tgcctataagttaatctgttatttgctgatcgtcttactgtgattgaactacag
||| ||||  ||||||||||| |   | |||||||||||||||||||| |||||||| || || || || || || ||  | |||||    ||||| |||||  | | | |  |  ||  |  |||   ||  |  ||| |   |  ||   |  ||||||| |                          
CGGCTTCAGCCAGAACCAGCTCATTCTCTGGAAGTACCCGTCGATGGTGAAGATGGCGGAGCTGACCGGGCACACCTCGAGGGTCCTGCATATGGCACAGgtctgctccctagtttttctttctttcttaggaaagtgcttgagacatacctttgtatttgcag--------------------------

upper sequence: LOC_Os02g47180.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ38024 (Selaginella moellendorffii), 5'ss of exon 3
CGGATTCACGCAGAACCAGCTGACATTGTGGAAGTACCCGTCGATGGTTAAGATGGCTGAACTCACTGGCCATACTTCCCGTGTCCTTTTCATGGCTCAGgtgagtttcttcttgattagtagttttg-cagtcactgcctataagttaatctgttatttgctgatcgtcttactgtgattgaactacag
 |||||||  ||||||||| |||  ||||||||||||||||| ||||| |||||||| ||||| || || || || ||| | ||| |   | |||| |||||   | |  ||||| || ||     || |||    |  ||| |      | ||||  |||| |                          
TGGATTCAGCCAGAACCAGTTGATCTTGTGGAAGTACCCGTCTATGGTGAAGATGGCGGAACTTACCGGTCACACGTCCAGAGTCTTGCACTTGGCGCAGgtagatgt--tcttgcttggtttccatgtcagctggtatcta-accacgctgtgttcgttgcag--------------------------

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|325493626|gb|JG458150.1|JG458150
EST:     AGATGGCTGAACTCACTGGCCATACTTCCCGTGTCCTTTTCATGGCTCAG                         AGTCCTGATGGTTGCACAAGTAGCATCGGCTGCTGCAGATGAGACCCTGCG
genomic: AGATGGCTGAACTCACTGGCCATACTTCCCGTGTCCTTTTCATGGCTCAGgtgagtttct ... tgaactacagAGTCCTGATGGTTGCACA-GTAGCATCGGCTGCTGCAGATGAGACCCTGCG
EST: gi|66915812|gb|CX102660.1|CX102660
EST:     GATGGCTGAACTCACTGGCCATAACT-CCCGTGTCCTTTTCATGGCTCAG                         AGTCCTGATGGTTGCACAGTAGCATCGGCTGCTGCAGATGAGAACCTGCGG
genomic: GATGGCTGAACTCACTGGCCATA-CTTCCCGTGTCCTTTTCATGGCTCAGgtgagtttct ... tgaactacagAGTCCTGATGGTTGCACAGTAGCATCGGCTGCTGCAGATGAGACCCTGCGG