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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcgacctcctaatccatcctactctataaatgtcataattctcacctgaatataacctgtgtaactaatttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g64660.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G836250_T02 (Zea mays), 3'ss of exon 5
---gtaatcgacc--tcctaatccatcc-tactctataaatgtcataattctcacctgaatataacc----tgtgtaactaatttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG
    ||| | |    | ||  |  | || |  |||   || || || ||    | |  |||||||      || | ||| ||| |||||||||| |||||||| ||||||| |||||||||||||||||| || || || || || |||||||||||| |||| |||||||||||||||
gtaataaccaattaattctcttgaacccatcttctccgaaggtaatcatctgtaacgaaatataattgacatgcgcaaccaatctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCACTTGGGGAGTTCATACTAACCCATCCAGACATCAAG

upper sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 6
---gtaatc--gacctcctaatccatcc----tactctataaatgtcataat---tctcacctgaatataacctg-----tgtaactaatttgat-gcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG
   | | ||  ||| |||   |   ||     |  | ||| ||| |  || |   | |    |   | |  |||      || |    | ||  | |||||||||  | || ||||||| |||||| ||||| || || ||||||||||| || |||||||||||| | ||||| ||| |||| |||
tctgcagtctagacttccatctttttctctggtgttgtattaatttggtactgcatttattttaggtgttgccttaattttgcattacacttatttgcagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG
















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|29682613|gb|CB678888.1|CB678888
EST:     GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|38473796|gb|CF957928.1|CF957928
EST:     NAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|58590217|gb|CF988525.1|CF988525
EST:     GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|38480766|gb|CF964855.1|CF964855
EST:     GAAAAAACATGGGTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|4714676|gb|AU055793.1|AU055793
EST:     GAAAAAACATGGTTGCNGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctataaatgtcataattctcacctgaatataacctgtgtaactaatttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG
                                      taactaattt  TA-rich tract