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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGAAGAACCTAACTATGCAAAGTGTATATCCCTTTTCGATACTGTAGTGGGCCCAAATCCAGATATCAGGCCAATTAACACCGATGGTGCTCAGAAGgtacaatacaatcatatattgcaatctgttatactgcttaaaaatcatgactttggttgcactaatcttccttgtaatttctctaaag

Basic information

species Oryza sativa
transcript LOC_Os01g54100.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G095634_T01 (Zea mays), 5'ss of exon 3
TGATGAAGAACCTAACTATGCAAAGTGTATATCCCTTTTCGATACTGTA---------GTGGGCCCAAATCCAGATATCAGGCCAATTAACACCGATGGTGCTCAGAAGgtacaatacaatcatatattgcaatctgttatactgcttaaaaatcatgactttggttgca-ctaatcttccttgtaatttctctaaag
         |||  |||||||||| |||  ||| |||||  ||| ||||         || ||  ||||||||||| |||| ||||||||||| ||||||||||||||||||        |||||| ||||| ||||| ||     | ||||  ||| | |||||||    |||| || ||||| |  ||||||||||
---------ACCCGACTATGCAAAATGTGCATCACTTTTTCATAGTGTACTAAGTGTAGTAGGTTCAAATCCAGATGTCAGACCAATTAACACTGATGGTGCTCAGAAGgtatgt-----tcatattttgca-tctgtcat----ttaaaaacacattattttggttttttctaacctcccttgcatcttctctaaag

upper sequence: LOC_Os01g54100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA04G09080.1 (Glycine max), 5'ss of exon 10
TGATGAAGAACCTAACTATGCAAAGTGTATATCCCTTTTCGATACTGTAGTGGGCCCAAATCCAGATATCAGGCCAATTAACACCGATGGTGCTCAGAAGgtac--aatacaatcat-atattgcaatctg-ttatactgcttaaaaatcatgactttggttgc-actaatcttcctt---gtaatttctctaaag
|||||||||||| || |||||||| | ||||||||||||||||    | ||||||||||||||||||||||||||||| ||||| || ||||||||||||||||  ||| | || || || ||  ||| || || || |||||| | ||    | | ||  ||  |||   |||  ||   || |||  |||  ||
TGATGAAGAACCAAATTATGCAAAATATATATCCCTTTTCGATGGAATTGTGGGCCCAAATCCAGATATCAGGCCAATAAACACTGAAGGTGCTCAGAAGgtacttaattctattattattttaaaatttgcttttattgcttacatatttaaagtctgactgtgactgccctttttttgggttattattctgtag

upper sequence: LOC_Os01g54100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA04G09070.2 (Glycine max), 5'ss of exon 10
TGATGAAGAACCTAACTATGCAAAGTGTATATCCCTTTTCGATACTGTAGTGGGCCCAAATCCAGATATCAGGCCAATTAACACCGATGGTGCTCAGAAGgtac--aatacaatcat-atattgcaatctg-ttatactgcttaaaaatcatgactttggttgc-actaatcttcctt---gtaatttctctaaag
|||||||||||| || |||||||  | ||||||||||||||||    | ||||||||||||||||||||||||||||| ||||| || ||||||||||||||||  ||| | || || || ||  ||| || || || |||||| | ||    | | ||  ||  |||   |||  ||   || |||  |||  ||
TGATGAAGAACCAAATTATGCAAGATATATATCCCTTTTCGATGGAATTGTGGGCCCAAATCCAGATATCAGGCCAATAAACACTGAAGGTGCTCAGAAGgtacttaattctattattattttaaaatttgcttttattgcttacatatttaaagtctgactgttactgccctttttttgggttattattctgtag

upper sequence: LOC_Os01g54100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA06G09190.1 (Glycine max), 5'ss of exon 10
TGATGAAGAACCTAACTATGCAAAGTGTATATCCCTTTTCGATACTGTAGTGGGCCCAAATCCAGATATCAGGCCAATTAACACCGATGGTGCTCAGAAGgtac--aatac-aatcatatattgcaatctg--ttatactgcttaaaaatcatgactttggttgcactaatcttcctt---gtaatttctctaaag
|||||||||||| || |||||||| | ||||||||||||||||    | ||||||||||||||||| ||||||||||| ||||| |||||||||||||||||||  ||| | |||  ||  ||  ||| ||  || || |||||| | ||    | | ||  ||   |   | |  ||   |  |||  |||  ||
TGATGAAGAACCAAATTATGCAAAATATATATCCCTTTTCGATGGAATTGTGGGCCCAAATCCAGACATCAGGCCAATAAACACTGATGGTGCTCAGAAGgtacttaatgctaatattactttagaatttgctttttattgcttacatattgaaagtctgactgttgttgcccttgtttgggctattattctgtag

upper sequence: LOC_Os01g54100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 10
TGATGAAGAACCTAACTATGCAAAGTGTATATCCCTTTTCGATACTGTAGTGGGCCCAAATCCAGATATCAGGCCAATTAACACCGATGGTGCTCAGAAGgta--caatacaatcatatattgcaatc-tgttatactgcttaa--aaatcatgactttggttgcactaatcttccttgtaatttctctaaag-------------------------------
||||||||||||||| |||||||| | ||| ||||| || |||    | || || ||||| ||||||||||||||||||||||| ||||||||||||||||||   | ||   || |   |      | ||| ||  | | | |   |        | |  ||    || | ||      | |||||  |  |                               
TGATGAAGAACCTAATTATGCAAAATATATTTCCCTCTTTGATGGGATTGTAGGTCCAAACCCAGATATCAGGCCAATTAACACAGATGGTGCTCAGAAGgtaactactatgctcttgcttctaggccgtgtgatggttcattattgagctggagttcttatttgtttattgtttaacagactttctgaatggagatctaatttatactctttttcttgtgaag

upper sequence: LOC_Os01g54100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 5'ss of exon 10
TGATGAAGAACCTAACTATGCAAAGTGTATATCCCTTTTCGATACTGTAGTGGGCCCAAATCCAGATATCAGGCCAATTAACACCGATGGTGCTCAGAAGgtacaa---tacaatcatatattgcaatctgttat--actgcttaaaaatcatgactttggt-tgcactaatcttccttgtaatttctctaaag
||||||||||||||| |||||||| | ||| ||||| || |||    | ||||| |||||||| |||||||||||||| ||||| |||||||||||||||||||     ||   | || | |    |     |||  | | |||   |    || ||||||  ||||   | | |   | ||  |  | | |||
TGATGAAGAACCTAATTATGCAAAATATATCTCCCTCTTTGATGGGATTGTGGGTCCAAATCCGGATATCAGGCCAATAAACACTGATGGTGCTCAGAAGgtacccatttatgtttatctgtctgtactgaatatgaatttcttttcacatttggctttggagtgcatctaacatgtatttacctattgtgaag

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|58688056|gb|CK076743.1|CK076743
EST:     TGGGCCCAAATCCAGATATCAGGCCAATTAACACCGATGGTGCTCAGAAG                         CTTATACATCTAGTTGGCCAAAAGAGAGGTCGCTTATTGATGGAAGAGACA
genomic: TGGGCCCAAATCCAGATATCAGGCCAATTAACACCGATGGTGCTCAGAAGgtacaataca ... ttctctaaagCTTATACATCTAGTTGGCCAAAAGAGAGGTCGCTTATTGATGGAAGAGACA
EST: gi|58680661|gb|CK069348.1|CK069348
EST:     TGGGCCCAAATCCAGATATCAGGGCAATTAACACCGATGGTGCTCAGAAG                         CTTATACATCT
genomic: TGGGCCCAAATCCAGATATCAGGCCAATTAACACCGATGGTGCTCAGAAGgtacaataca ... ttctctaaagCTTATACATCT