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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttttttctctaataatcacagtaatgcagctggcatttgactgttgtcccctaatgttcctgttctatattaaacagttctgggttgattgtgatagGTCGAAGAATCTTGTTGCACTTTGAAGCTGTTGATTCAGCGTTTTTTGCTTGGGTAAACGGCGTTCCTGTTGGATATAG

Basic information

species Oryza sativa
transcript LOC_Os01g72340.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g72340.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G26700.1 (Glycine max), 3'ss of exon 3
cttttttttctctaataatcacagtaatgcagctggcatttgactgttgtcccctaatgttcc-tgttctatattaaacagttctgggttgattgtgatagGTCGAAGAATCTTGTTGCACTTTGAAGCTGTTGATTCAGCGTTTTTTGCTTGGGTAAACGGCGTTCCTGTTGGATATAG
 || || || | |     |     | | |   ||| || |    |  |||   ||| | |    |  |  ||  |    |    ||  | | || || ||||| ||||| | |||||||| |||||||| |||||||| || |||| ||| ||| |||| ||   |||||||||||||||
tttgttgttatattcctgttggttttaagtctctgtcagt-actttctgttttctagtctaaaatacttaattctttggaacattgattggtttttggtagGTAGAAGAGTTTTGTTGCATTTTGAAGCAGTTGATTCTGCCTTTTGTGCATGGATAAATGGGCATCCTGTTGGATATAG

upper sequence: LOC_Os01g72340.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv13s0067g03000.t01 (Vitis vinifera), 3'ss of exon 3
cttttttttctctaataat-cacagtaatgcagctg-gcatttgactgttgtcccctaatgttcctgttctatattaaacagttctgggttgattgtgatagGTCGAAGAATCTTGTTGCACTTTGAAGCTGTTGATTCAGCGTTTTTTGCTTGGGTAAACGGCGTTCCTGTTGGATATAG
 |||    | | || || | |||  ||||  |  || | |    | ||   |  ||||||| ||   | ||  |||||    | |    ||     ||| |||||| || || ||||| |||||||||||||||||||| || |||||||| ||| |||| || |||||||||||||||||
-tttaaagtttttagtatttcaccctaattaaaatgtgtaaaatattga-atgtcctaatgctctcttccttaattaagttatgcaaatttacacttgacagGTCGTAGGATATTGTTACACTTTGAAGCTGTTGATTCTGCCTTTTTTGCATGGATAAATGGAGTTCCTGTTGGATATAG
















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|29621652|gb|CB626663.1|CB626663
EST:     TCCTACTGGCTGTTATAGGACGGTTTTTCGCATCCCAAAAGAGTGGAAAG                         GTCGAAGAATCTTGTTGCACTTTGAAGCTGTTGATTCAGCGTTTTTTGCTT
genomic: TCCTACTGGCTGTTATAGGACGGTTTTTCGCATCCCAAAAGAGTGGAAAGgtatgatatg ... attgtgatagGTCGAAGAATCTTGTTGCACTTTGAAGCTGTTGATTCAGCGTTTTTTGCTT
EST: gi|86904819|gb|CI310612.1|CI310612
EST:     TCCTACTGGCTGTTATAGGACGGTTTTTCGCATCCCAAAAGAGTGGAAAG                         GTCGAAGAATCTTGTTGCACTTTGAAGCTGTTGATTCAGCGTTTTTTGCTT
genomic: TCCTACTGGCTGTTATAGGACGGTTTTTCGCATCCCAAAAGAGTGGAAAGgtatgatatg ... attgtgatagGTCGAAGAATCTTGTTGCACTTTGAAGCTGTTGATTCAGCGTTTTTTGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtcccctaatgttcctgttctatattaaacagttctgggttgattgtgatagGTCGAAGAATCTTGTTGCACTTTGAAGCTGTTGATTCAGCGTTTTTTGCTTGGGTAAACGGCGTTCCTGTTGGATATAG
                  tgttctatattaaa  TA-rich tract