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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAAAGAGTATGAAATGGCTCTTCAGGACAGGGTGATGGAAGAGACAAAAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcgattccactctttcctgacttcatctttagttagaggcagaaactgataatatgttatttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g08560.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08560.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G22100.1 (Glycine max), 5'ss of exon 5
GGAAAAAGAGTATGAAATGGCTCTTCAGGACAGGGTGATGGAAGAGACAAAAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcgat---tccactctttcctgacttcatctttagttagaggcagaaactgataatatgttatttttcag-------------------------
 ||||| |||| |||||||||| | || ||  | ||||||||||| |||||||| ||||| ||||| || ||| ||||||||||||||||| ||||||||||  |    ||   |    ||||  || |||     | ||     |   | |||    |   || | ||| || |                          
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGTGTGATGGAAGAAACAAAAGACAAGAAAAATGCAGTTGAGGCTTATGTTTATGACATGAGAAACAAGgtgggtgttatctttttcttcttctcttactcagggtctaacatcaactacaaatgcctgtcatataattgttgatttttttttttccgttatcatttcag

upper sequence: LOC_Os01g08560.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G00820.1 (Glycine max), 5'ss of exon 5
GGAAAAAGAGTATGAAATGGCTCTTCAGGACAGGGTGATGGAAGAGACAAAAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcgattccactctttc-ctgacttcatctttag--ttagaggcagaaactgataatatgttatttttcag------------------------
 || || |||| |||||||||| | || ||  | ||||||||||| |||||||| ||||| || || || ||| ||||||||||||||||| ||||||||||  |  | ||    ||  ||| || ||      | ||   | | |  || |  |   | ||||  || || |                           
AGAGAAGGAGTTTGAAATGGCTTTGCAAGATCGTGTGATGGAAGAAACAAAAGACAAGAAAAACGCAGTTGAGGCTTATGTTTATGACATGAGAAACAAGgtgggcgctatctttcttgttctcttacccagggtctaacatcacatacaaatgcctgtcatataataattgttgattttttttcctgttatcatttcag

upper sequence: LOC_Os01g08560.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA15G01750.1 (Glycine max), 5'ss of exon 6
GGAAAAAGAGTATGAAATGGCTCTTCAGGACAGGGTGATGGAAGAGACAAAAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttg-atcgattccactctttcctgacttcat------ctttagttagaggcagaaactgataatatgttatt-tttcag
 || || |||| |||||||||| | || || || |||||||| || ||||| |||||||| ||||| || ||| ||||||||||||||| | ||||||||||  | || |       | | |  | | || |        |||   |     |  ||||| ||      ||||  ||||||
AGAGAAGGAGTTTGAAATGGCTTTGCAAGATAGAGTGATGGAGGAAACAAAGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAGgtgaggattgccatggttttcttgttatttaaggatgaattttgtattattactaaaactaatttctcattatcatttcag

upper sequence: LOC_Os01g08560.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA13G43630.2 (Glycine max), 5'ss of exon 6
GGAAAAAGAGTATGAAATGGCTCTTCAGGACAGGGTGATGGAAGAGACAAAAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgt-----ttgat-cgattccactctttcctga---------cttcatctttagttagaggcagaaactgataatatgttatt-tttcag
 || || |||| |||||||||| | || || || || ||||| || || ||||||||||| ||||| || ||| ||||||||||||||||| ||||||||||     |||    | ||    | ||   |||          || || |||| |||    |  ||||| ||    || |||  ||| ||
AGAGAAGGAGTTTGAAATGGCTTTGCAAGATAGAGTCATGGAGGAAACGAAAGATAAGAAAAATGCAGTTGAGGCTTATGTTTATGACATGAGAAACAAGgtgaggattgccatggttttcttgttatttgaggtcaatttttttatttttaattatta-ctaaaactaatttcttgatatcattttag

upper sequence: LOC_Os01g08560.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G79930.1 (Arabidopsis thaliana), 5'ss of exon 6
GGAAAAAGAGTATGAAATGGCTCTTCAGGACAGGGTGATGGAAGAGACAAAAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttga---tcgattccactctttc-ctgacttcatctttagttagag--gcagaaactga----taatatgttat-ttttcag
||| || || | ||| |||||| | || ||||| || ||||||||||| || ||   ||||||||| || ||||||||||||||||| ||||| ||||| ||  ||   |  ||| |    ||||  || |   ||   ||  || ||  |     | ||     |||  |||  | |||||||
GGAGAAGGAATTTGAGATGGCTTTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAAgtgagaatctttatttcgtcttttcattggcagtatgcatatgtaaagttgtgagtattgggtactaacgtgtcttgttttcag

upper sequence: LOC_Os01g08560.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G79920.2 (Arabidopsis thaliana), 5'ss of exon 6
GGAAAAAGAGTATGAAATGGCTCTTCAGGACAGGGTGATGGAAGAGACAAAAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttga----tcgattccactctttc-ctgacttcatctttagttagag------gcagaaactgataatatgttat-ttttcag
||| || || | ||| |||||||| || ||||| || ||||||||||| || ||   ||||||||| || ||||||||||||||||| ||||||||||| ||  ||    |  ||| |    ||||  || |   ||   ||  || ||      | |   | |  | |  |||  | |||||||
GGAGAAGGAATTTGAGATGGCTCTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGAAACAAAgtgagaaatctttatttcgtcttttcattggcagtatgcatatgtaaagttttgagtattgagtactgacgtgtcttgttttcag

upper sequence: LOC_Os01g08560.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 5
GGAAAAAGAGTATGAAATGGCTCTTCAGGACAGGGTGATGGAAGAGACAAAAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttga---tcgattccactcttt----cctgacttcatctttagttagaggcagaaactgata-----atatgttatttttcag------
 ||||| |||| |||||||||| | || ||  | || |||||||| |||||||| |||||||||||||||||| | ||||||||||||||| ||||||||||  |    || || | | |   |    |   | | || | || || |    ||   |||||||     | ||| |  | ||| |      
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgtttctatcctattggctaagacagaattacagcatttgtaaccttcacctactgatatctacacatgattatcttctgccccag

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|58677519|gb|CK066206.1|CK066206
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
EST: gi|218481790|gb|FG945721.1|FG945721
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
EST: gi|58597595|gb|CK008123.1|CK008123
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACGAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACCAGGAAGCATTC
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
EST: gi|2310021|gb|C26176.1|C26176
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
EST: gi|29636673|gb|CB641682.1|CB641682
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
EST: gi|27553959|gb|CA997859.1|CA997859
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
EST: gi|86831930|gb|CI303370.1|CI303370
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
EST: gi|29619080|gb|CB624092.1|CB624092
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCT
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCT
EST: gi|86829544|gb|CI286738.1|CI286738
EST:     AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACGAG                         CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC
genomic: AAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcga ... tatttttcagCTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAAAAGAGTATGAAATGGCTCTTCAGGACAGGGTGATGGAAGAGACAAAAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttgatcgattccactctttcctgacttcatctttagttagaggcagaaactgataatatgttatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG