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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttgatccctgccctctcatcttcatttcctcagctcttgcttcaaatggttgttacctgactgtcatcccacctccattttctgctcag

Basic information

species Oryza sativa
transcript LOC_Os02g54510.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54510.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G039106_T03 (Zea mays), 5'ss of exon 4
TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttgatccctgccctctcatcttcat---ttcctcagctcttgcttcaaatggttgttacctgactgtcatcccacctccattttctgctcag------------------
|||||||||||||||||| |||||||||||||| |||||||| || ||||||||||| |||||||| ||||||||||||||||| |||||||||||||| ||||||||||| |||   | | | | |      ||      ||      |||  ||||  |    |||     |  |  |    |||| | ||                   
TGGCATGGAATATTTGCACGGGAAGAATATAGTCCATTTTGACCTGAAGTGTGAGAATCTACTGGTGAACATGAGGGATCCACAGCGACCAATCTGCAAGgtttgatcccttccccagcctttccctacgccgctttatctttctggggaattcttgtcgcaatgctggatatcttctcctgacttctccccaacacaaatactctgatcag

upper sequence: LOC_Os02g54510.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G052658_T01 (Zea mays), 5'ss of exon 5
TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttgatccctgccctctcat-------cttcatttcctcagctcttgct-tca-aatggttgttacctgactgtcatcccacctc---cattttctgctcag
||||||||| ||||||||||||||||||||||| |||||||| || || |||||||| |||||||| |||||||||||||| || |||||||| ||||| ||||||||||   ||| ||         ||| || |     |   ||| | ||| |||||| | | ||||||| |   || | |||    | | |||| ||||
TGGCATGGAGTATTTGCATGGGAAGAATATAGTCCATTTTGACCTGAAATGTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAGgtttgatccccagcctttccctctgctgctttatctttctggaaattgttgtcacaatggtggat-cctgact-tgtcccaaactcaaatactctctgatcag

upper sequence: LOC_Os02g54510.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA13G01190.2 (Glycine max), 5'ss of exon 8
TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttg-atccctgccctctcatcttcatttcctcag-ctcttgcttcaaatggt-tgttacctga--ctgtcatcccacctccattttctgctcag
||| ||||| ||||||||||| || || || |||||||||||| | || |||||||| ||| ||||||| ||||| ||||| ||||| || |||||||| ||    ||       |   ||  | || |    ||| |    ||   ||      || || | ||   ||  ||   |  |   |  | |  ||||
TGGGATGGAGTATTTGCATGGAAAAAACATTGTTCATTTTGATTTGAAATGTGAGAATCTATTGGTCAATATGAGAGATCCTCAACGGCCTATCTGCAAGgtacacataagaatacatacacatacactgatgcagacaaaagccaaaagcaacctgctagcggagattgaaatgagatttgtgtaattt-ttcag

upper sequence: LOC_Os02g54510.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA17G07320.1 (Glycine max), 5'ss of exon 11
TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttg-atccctgccctctcatcttcatttcctcagctcttgcttcaaatggt-tgttacctga--ctgtcatcccacctccattttctgctcag
||| ||||| ||||||||||| || || || || ||||||||| | || |||||||| ||| ||||||| ||||| ||||| ||||| || |||||||| ||    ||       |  |||  |  | |    || |    ||   |       || || | ||   ||  ||   |  |   |  | |  ||||
TGGGATGGAGTATTTGCATGGAAAAAACATTGTGCATTTTGATTTGAAATGTGAGAATCTATTGGTCAATATGAGAGATCCTCAACGGCCTATCTGCAAGgtacacataagaatacattcacatatactgaggcaacaaaagccaaacgcaacctgctagcggagattgaaatgagatttgtgtaattt-ttcag

upper sequence: LOC_Os02g54510.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT5G57610.1 (Arabidopsis thaliana), 5'ss of exon 6
TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttgatccctgccc-tctcatct-tcatttcctcagctcttgcttcaaatggttgttacctgactgtcatcccacctccattttctgctcag
||| ||||| |||||||| || ||||| || |||||||| ||| | ||||||||||| || || || |||||||| ||||| || || || || ||||| |||   |   | | | ||| |||| |||| |    |    |    | | ||| || | |  | | | |  |    | | | |||||    |||
TGGGATGGAGTATTTGCACGGAAAGAACATTGTTCATTTCGATTTGAAGTGTGAGAATCTTCTTGTGAACATGAGAGATCCTCAGCGTCCTATATGCAAGgttctgttgttactcatctgatctctcatataacaaagagtaagcttatatgtttctca--taaattttgt----ctttctttttccttccag

upper sequence: LOC_Os02g54510.2 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ30928 (Selaginella moellendorffii), 5'ss of exon 3
TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtt-tgatccctgccctctcatcttcatttcctcagctcttgcttcaaatggttgttacctgactgtcatcccacctccattttctgctcag
||| ||||| ||| | || || ||||| || |||||||| || || ||||| |||||  | ||||||||||||||||||||||| || ||| | ||||| ||  ||||  ||  | ||||   ||| ||  ||  |   |   |     ||   ||| || |                              
TGGGATGGAGTATCTACACGGAAAGAACATCGTTCATTTCGACCTGAAGTGCGAGAATTTGCTGGTCAACATGAGGGATCCACATCGGCCAGTGTGCAAGgtaatgatatct-tcgtctctcgttctttcactttgtagtgagtgactgtgcacgtttccag------------------------------

upper sequence: LOC_Os02g54510.2 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ17246 (Selaginella moellendorffii), 5'ss of exon 3
TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtt-tgatccctgccctctcatcttcatttcctcagctcttgcttcaaatggttgttacctgactgtcatcccacctccattttctgctcag
||| ||||| ||| | || || ||||| || |||||||| || || ||||| |||||  | ||||||||||||||||||||||| || ||| | ||||| ||  ||||  ||  | ||||   ||| ||  ||  |   |   |     ||   ||| || |                              
TGGGATGGAGTATCTACACGGAAAGAACATCGTTCATTTCGACCTGAAGTGCGAGAATTTGCTGGTCAACATGAGGGATCCACATCGGCCAGTGTGCAAGgtaatgatatct-tcgtctctcgttctttcgctttgtagtgagtgactgtgcacgtttccag------------------------------

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|396941216|gb|HO188425.1|HO188425
EST:     GGTCAACATGAGGGATCCACAACGACCAATCTGCAAA                         ATTGGTGATCTTGGACTATCAAAGGTGAAGCAGCACACTTTGGTGTCTGGC
genomic: GGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttgatccc ... ttctgctcagATTGGTGATCTTGGACTATCAAAGGTGAAGCAGCACACTTTGGTGTCTGGC
EST: gi|66924155|gb|CX111003.1|CX111003
EST:     GTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAA                         ATTGGTGATCTTGGACTAT
genomic: GTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttgatccc ... ttctgctcagATTGGTGATCTTGGACTAT