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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcactattcaccaaatgatcatctatatccttatcattcatctagcaacaatatttatgtaatctgcaggtccag

Basic information

species Oryza sativa
transcript LOC_Os11g04980.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04980.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA20G28200.1 (Glycine max), 5'ss of exon 6
TGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcactattca--ccaaatgatcatctatatccttat-cattcatctagcaacaatattta--tgtaatctgcaggtccag------------
 | ||||| ||||||||||| ||||||||||||||| |||| ||||||||||| ||  | ||||| ||||| || || ||||| || ||||| ||||||||||||   | | ||    |  ||   || | | | ||||   ||  | || |     |  || |  | |||     ||   | |            
AGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTGCATACTCATTTGTATCAGTGCCTCTGTATGATACTCTTGgtatgttgtctacaatttatctggaaatttcttttcttacatatctaccttggccttaccttcagatttaacagcaagaaactgcttgttctgtag

upper sequence: LOC_Os11g04980.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA15G34650.1 (Glycine max), 5'ss of exon 2
----------------------TGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtat--gcactattcaccaaatgatcatct-atatccttatcattcatctagcaacaatatttatgtaatctgcaggtccag
                       | ||||| ||||||||||| ||||||||||||||| |||| ||||||||||| ||  | ||||| ||||| |||   ||   | ||| ||  ||       ||    | ||||    |  |  |  ||  |||| |  |   | ||||||   |   ||                      
TTATGGAATCCAAAAGGGCTCTAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTGCATACTCATTTGTGCAAgttatattttgtg-tacctcaaacattaaaattattgctgagctacttgtcagatattccaactgtacatctaatcatggtag---------------------

upper sequence: LOC_Os11g04980.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 6
TGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgc-----actattcaccaaatgatcatctatatccttatcattcatctagcaacaatatttatgtaatctgcaggtccag-------------
 | ||||| ||||||||||| ||||||||||||||| |||| ||||||||||| ||  |  |||| ||||| || || ||||| || ||||| |||||||||| ||     |  ||| | ||    ||  ||| |      ||   |    | ||   |   | |   | | | ||| |                  
AGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTTCATACTCATTTGTATCAGTGCCTCTGTATGATACTCTTGgtacgctgtctataatttatcaggaaatt-tcttttcttacatgtctaccttggccttaccttctgatttaacagcaagaaattgcttgttctgtag

upper sequence: LOC_Os11g04980.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 5'ss of exon 6
TGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcactattcaccaaatgatca-tctatatccttatcattcatctagcaacaatattt----atgtaat-ctgcaggtccag---
||| ||||  | |||||||| |||||||| |||||| |  | || |||||||| ||||||||||||||||| || ||||| ||  | ||||| || |||||||  || | |  |    ||  |   ||| ||   ||    ||   | |||        ||    || | || || | |||   |   
TGCGTTGGACTCTATTTTATTAACAGACCAGAGTGGTTGGTTGTGGATCATGCTTGTGCAGCATATTCATTTGTCTCTGTTCCTTTATATGATACACTTGgtaaccaatctaaatttgattttttctctttagttttcgagttttgcaagccttgtctcttcttaatatgattcttctggttacgcag

upper sequence: LOC_Os11g04980.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 6
TGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgca-ctattcaccaaatgatcatctat-atccttatcattcatctagcaacaatatttatgtaa-tctgc--aggtccag----------------------------
||  ||||  | |||||||| ||||||||||||||| |||| ||||||||||||||  | |||| |||||  || || || ||  | |||||||||||||||  | |  |  | |    || |   | |||    ||| |   |    | || | |  | |  |  || ||| |  | |   |                             
TGTGTTGGCCTATATTTTATCAACAGACCTGAGTGGCTCATTGTTGATCATGCCTGCTCTGCATTTTCATATGTATCAGTTCCTTTATATGACACTCTTGgttcgtaattggttattgtataaaactttatcggacttttgcctagcttggccaaaccactgctacaaatctactaaagcttaacaaagccttgataattgttgctctgcag

upper sequence: LOC_Os11g04980.2 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S408_23V6.1 (Physcomitrella patens), 5'ss of exon 8
TGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcactattcaccaaatgatcatctatatccttatcattcatctagcaacaatatttatgtaatctgcaggtccag---------------------
||  ||||  | ||  | || ||  || | || ||| ||||    || |  || ||||  || ||||| |  |||||||| |||||||||||||||||||||| ||   |  |  |     |  ||| | ||       | |     |    |  ||||| | |    | |    | |                      
TGTGTTGGAATATACATGATCAATCGAGCAGAATGGGTCATCTCAGAACTAGCATGTGTCGCTTATTCCTATGTGTCTGTTCCACTTTATGACACTCTTGgtaagctgcacccttctctgaaatatcaacattgaacagactagctaaatgtctttatttgtctcgatttcgtaactaatcagactcttagttttgagtt

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|33676001|gb|CF304240.1|CF304240
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGGTCCAG                    
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTC-T--T---Ggtatgcacta ... gcagg
EST: gi|58696224|gb|CK084911.1|CK084911
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGGTCCAG                    
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTC-T--T---Ggtatgcacta ... gcagg
EST: gi|29671403|gb|CB667678.1|CB667678
EST:     CGTGTCTGTGCCACTTTATGACACTCTTGGTCCAG                    
genomic: CGTGTCTGTGCCACTTTATGACACTC-T--T---Ggtatgcacta ... gcagg
EST: gi|58690407|gb|CK079094.1|CK079094
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         G
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... gcaggtccag-
EST: gi|58690407|gb|CK079094.1|CK079094
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         G
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... gcaggtccag-
EST: gi|58690407|gb|CK079094.1|CK079094
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         G
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... gcaggtccag-
EST: gi|58690407|gb|CK079094.1|CK079094
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         G
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... gcaggtccag-
EST: gi|58690407|gb|CK079094.1|CK079094
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         G
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... gcaggtccag-
EST: gi|58663800|gb|CK052486.1|CK052486
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGGTCCAG                    
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTC-T--T---Ggtatgcacta ... gcagg
EST: gi|33675052|gb|CF303291.1|CF303291
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGGTCCAG                    
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTC-T--T---Ggtatgcacta ... gcagg