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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgttagtatacagttcttttgtttctttgctacataacatgtggctttgacctcatacttggtgaaccaacgtttaagtttggtgtggtctacatgaatataacttcattatctgatttgcgttgatttctgctgcctttag

Basic information

species Oryza sativa
transcript LOC_Os09g28570.3
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g28570.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G368058_T01 (Zea mays), 5'ss of exon 6
GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgttag-----tatacagttcttttgtttctttgctacataacatgtggctt-tgacctcatacttggtgaaccaacgtttaagtttggtgtggtctacatgaatataacttcattatctg---atttgcgtt-gatttctgctgcctttag--------
 || |||||||   |||| |||| |||||||||||||| |||||||| ||||||||||||||||||||||||||||| || || || ||||| ||||||       |  | | |||||   ||| |   |    |  ||| || | | |    | ||   |  ||     || |   | |    |      |      |||||| ||  ||   ||   || ||  || ||||| |||||| |||          
ATTTCAGCCAAAAGTCTTATTCCAGTGCCAAGACCAGACCCAGAGGTGGTTGCTATGCTAACATCAGGATTGACTGCATCCATCGCTCTTGAAAAGgttctgttcctccatatttcttagttttttccacggtttggcatatgccatgtatttttatctctattgtgttcacataagattcaaattccaagtttgaagatataattttcttccttgcttatctggattcgatttatgctgcatttcttccattag

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G147191_T02 (Zea mays), 5'ss of exon 11
GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgttagtatacagttcttttgtttctttgctacataacatgtggctttgacctc-atacttggtgaaccaacgtttaagtttggtgtggtctacatgaatataacttcattatctgatttgcgttgatttctgctgcctttag
||||||||||| ||||||||||| |||||||||||||| || ||||| ||||| ||| | ||||||||| ||||||| ||||||   ||||| ||||||  | |    | |   || || ||| ||  |           | ||   || || ||   | ||     | || | ||| |   | | ||                                                  
GTTCCAGCCAAACATCTTCTTCCAGTGCCAAGACCAGACCCTGAGGTTGTTGCAATGTTGACATCAGGACTGACTGCATCAATTAGTCTTGAAAAGgtttattttatatacccctgcttgttttctttacttttgagcaatctgttttctatcctaaattaatt--tggttgatttttgctggctttag-------------------------------------------------

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA02G15070.1 (Glycine max), 5'ss of exon 11
GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgttagtatacagttcttttgtttctttgctacataacatgtggctttgacctcatacttggtgaaccaacgtttaagtttggtgtggtctacatgaatataacttcattatctga----tttgcgttgatttctgctgcctttag------------------------
 ||||  | || |||  |||||||||||| ||||||||||| || || ||||| ||||| ||||| ||||||||||| |||||||| || || ||||||    ||   |  | |||| || ||||| ||  |  | |   | |  | |  || ||  |  ||  |  ||| |  |   |||     |      | |    | ||  ||||      || |  ||  || |  ||     ||                        
ATTCCTTCAAAACATGCTCTTCCGGTGCCTAGACCAGATCCTGAAGTTGTTGCCATGCTTACATCGGGATTGACTGCCTCAATTGCTCTAGAAAAGgttgac-taatataatgttgtctccttgcttca-gatgtatccttatttcttagtatttattatactcatctttgatatcaatgtaaatcaagccttttttttattatcttctgtgaatcttccactggcttgtcttgatcaaagtttccttttttgtacactcaaaag

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G49670.1 (Arabidopsis thaliana), 5'ss of exon 11
GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgt--tagtatacagttcttttgtttctttgcta-cataacatgtggctttgacctcatacttggtgaaccaacgtttaagtttggtgtggtctacatgaatataacttcattatctgatttgcgttgatttctgctgcctttag-------------
||  |  | |||||| ||||||| || ||||||||||||||||| || ||||| ||||| || || ||||| ||||| | ||| |||||||| |||||  |  ||   |||    ||   | | || |  |||    | |   ||    |||  |  |     |     || |   ||    |  || |  ||     ||| ||  |  |   |||  |  |||  | | ||   | |               
GTATCTTCTAAGCATGTTCTTCCTGTTCCAAGACCAGATCCAGAAGTTGTTGCCATGCTTACCTCGGGATTAACTGCATTAATCGCCCTTGAAAAGgtcgtgctaacgagtgtcattaactgtctgttttcatcgtttttcatttcagactctcaaattcctcatttttgtatgtattaatagctgtatg-atattcttaagttgctagttcaattatctctgacattttctttatcttatgggaattcacag

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G49670.2 (Arabidopsis thaliana), 5'ss of exon 11
GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgt--tagtatacagttcttttgtttctttgctacataacatgtggctttgacctcatacttggtgaaccaacgtttaagtttggtgtggtctacatgaatataacttcattatctgatttgcgttgatttctgctgcctttag
||  |  | |||||| ||||||| || ||||||||||||||||| || ||||| ||||| || || ||||| ||||| | ||| |||||||| |||||  |  ||   |||    ||   | | || |      |||  |  ||| |  ||| |||     |  |  | |||  || ||   |  |                                                     
GTATCTTCTAAGCATGTTCTTCCTGTTCCAAGACCAGATCCAGAAGTTGTTGCCATGCTTACCTCGGGATTAACTGCATTAATCGCCCTTGAAAAGgtcgtgctaacgagtgtcattaactgtctgtttt----cat-cgtttttcatttcagactctcaaattcctcatttttgtatgtattaatag---------------------------------------------------

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv03s0063g00610.t01 (Vitis vinifera), 5'ss of exon 11
GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgttagta--tacagttcttttgtttctttgctacataacatgtggctttgacctcatacttg---gtgaaccaacgtttaagtttggtgtggtctacatgaatataacttcattatctgatttgcgttgatttctgctgcctttag-------------------------------------------------
|||||  |||||||  | ||||| ||| |||||||||||||||| || ||||| |||||||| |||||| | || || ||||||||  | || |||||  ||   | ||  | | |    || |||    | |   |||   ||  |    ||   ||    ||     |  ||||  ||        ||   |    | |  | |  | ||    | | | ||  |||   |  || |||                                                  
GTTCCTTCCAAGCACATCCTTCCCGTGGCAAGACCAGATCCAGAAGTTGTTGCGATGCTAACCTCAGGACTTACAGCATCAATTGCTTTAGAAAAGgtatgttacttcaagtgtctgtcctccttgtccaagattttgttaattgcaatatatgtatgtaaatgtttatatatttacattcaactaattcattaattttctggccttctgatgctgtattctttctttttgtcatccattactgagacagttaattgtcttgttctgacaattcttttatggaacttgtag

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|58684560|gb|CK073247.1|CK073247
EST:     TCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG                         GCAGGCCAAATGGCATCAGGGCAAGTTGTTCTAGTTACAGCTGCTGCTGGT
genomic: TCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAGgttagtatac ... ctgcctttagGCAGGCCAAATGGCATCAGGGCAAGTTGTTCTAGTTACAGCTGCTGCTGGT