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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATACGTGCTCACCACGCCGCTCTACTACGTCAACGCCCCGCCGCACATGGGGAGCGCCTACACCACCATTGCCGCCGACGCCATCGCCCGCTTCCAGgcaagcaactaaagcgagcaagcctatgcgcgcgcgtttgcgttccattgctgctcgcgttctaatcccagtctagggattttgagtacgtcaaactgtt...

Basic information

species Oryza sativa
transcript LOC_Os03g11120.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11120.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G029055_T02 (Zea mays), 5'ss of exon 1
GCCATACGTGCTCACCACGCCGCTCTACTACGTCAACGCCCCGCCGCACATGGGGAGCGCCTACACCACCATTGCCGCCGACGCCATCGCCCGCTTCCAGgcaagcaactaaagcgagcaagcctatgcgcgcgcgtttgcgttccattgctgctcg--cgttctaatcccagtc-tagggattttgagtacgtcaaa-ctgtt
||| |||||||||||||| || ||||||||||||||||| |||||||| ||||| ||||||||||||||||| || || |||||||||||||||||||||||||||  | |   |   | |    | |||   |  |||  |  |  ||  |  |||  | | | ||  | | |   |        |  | |   | | |   |
GCCCTACGTGCTCACCACTCCTCTCTACTACGTCAACGCTCCGCCGCATATGGGAAGCGCCTACACCACCATCGCAGCGGACGCCATCGCCCGCTTCCAGgcaagcctcca---cccacgattgca-gcggctgtatttttgaacagttagttgtcgaacctacaaaagcaaattgcacatgcccgggttgcacgagatccact

upper sequence: LOC_Os03g11120.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA20G23250.1 (Glycine max), 5'ss of exon 1
GCCATACGTGCTCACCACGCCGCTCTACTACGTCAACGCCCCGCCGCACATGGGGAGCGCCTACACCACCATTGCCGCCGACGCCATCGCCCGCTTCCAGg--caagcaactaaagcgagcaagcctatgcgcgcgcgtttgcgttccattgctgctcgcgttctaatcccagtctagg--gattttgag--tacgtcaaactgtt
 |  |  || ||||| || || |||||||||||||| || || || |||||||| ||||| ||||||||||| || ||||| ||||| || ||||||||||  |||    |||   | | |   |  ||        ||||   ||    ||   ||   || | | |||     | ||  || || ||   |     |||||| |
ACACTTTGTCCTCACTACCCCTCTCTACTACGTCAATGCTCCTCCCCACATGGGTAGCGCTTACACCACCATCGCTGCCGATGCCATTGCTCGCTTCCAGgttcaattctctatctctacc---ctcattgattttagtttaaatta---tgtaactttggtccaattccagaaatgggtcgacttggaaattggactaaactgct

upper sequence: LOC_Os03g11120.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA10G43550.1 (Glycine max), 5'ss of exon 1
GCCATACGTGCTCACCACGCCGCTCTACTACGTCAACGCCCCGCCGCACATGGGGAGCGCCTACACCACCATTGCCGCCGACGCCATCGCCCGCTTCCAGgcaagc--aactaaagcgagca----------------agcctatgcgcgcgcgtttgcgttccattgctgctcgcgttctaatcccagtctagggattttgagtacgtcaaactgtt-------------------------
 || |  || ||||| || || ||||| |||||||| ||||| || |||||||| || || ||||||||||| |||||||| ||||| || ||||||||||  | |  | |||   | | |                 |   ||||       | |    |||||    || | | ||| |||        |      | | ||||| | | | | |                          
ACCCTTTGTCCTCACTACTCCTCTCTATTACGTCAATGCCCCTCCTCACATGGGTAGTGCTTACACCACCATCGCCGCCGATGCCATTGCTCGCTTCCAGgttaacttatctatctctaccctcattgattttagtttaaattatgtaactttggtccaattccagaaatgttggtgttttaactgtttattttctcctattagtacataataatataaggtttgcatagttgaatttgacag

upper sequence: LOC_Os03g11120.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv13s0019g00810.t01 (Vitis vinifera), 5'ss of exon 1
GCCATACGTGCTCACCACGCCGCTCTACTACGTCAACGCCCCGCCGCACATGGGGAGCGCCTACACCACCATTGCCGCCGACGCCATCGCCCGCTTCCAGgcaagcaactaaagcgagcaagcctatgcgcgcgcgtttgcgttccattgctgctcgc-gttctaatcccagtc-tagggattttgagtacgtcaaactgtt
  | | ||| ||||| || ||||| || ||||| || ||||| || |||||||| || ||||||||||| ||||| || |||||||| || || || |||| |  |   |     ||       |    |    ||  | |||   |  | || | |   || |  |  || |  |  || |  |||| | |   |      
TTCTTTCGTCCTCACGACTCCGCTTTATTACGTAAATGCCCCTCCCCACATGGGAAGTGCCTACACCACTATTGCTGCTGACGCCATTGCTCGATTTCAGgtaccctgttgtt-tgatttcttttgattgtattcggcttcgtggaagggatgattgttattttgttaacatttgtttggttggtgagaaagcggagaaaa-

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|29618323|gb|CB623335.1|CB623335
EST:     TGGGGAGCGCCTACACCACCATTGCCGCCGACGCCATCGCCCGCTTCCAG                         AGGTTGCTGGATAAGAGGGTCGTATTTATTACCGGAACAGATGAGCATGGC
genomic: TGGGGAGCGCCTACACCACCATTGCCGCCGACGCCATCGCCCGCTTCCAGgcaagcaact ... atggtcgcagAGGTTGCTGGATAAGAGGGTCGTATTTATTACCGGAACAGATGAGCATGGC
EST: gi|29619403|gb|CB624415.1|CB624415
EST:     TGGGGAGCGCCTACACCACCATTGCCGCCGACGCCATCGCCCGCTTCCAG                         AGGTTGCTGGATAAGAGGGTCGTATTTATTACCGGAACAGATGAGCATGGC
genomic: TGGGGAGCGCCTACACCACCATTGCCGCCGACGCCATCGCCCGCTTCCAGgcaagcaact ... atggtcgcagAGGTTGCTGGATAAGAGGGTCGTATTTATTACCGGAACAGATGAGCATGGC
EST: gi|58606716|gb|CK034749.1|CK034749
EST:     GGGGAGCGCCTACACCGAGCATTGCCGCCGACGCCATCGCCCGCTTCCAG                         AGGTTGCTGGATAAGAGGGTCGTATTTATTACCGGAACAGATGAGCATGGC
genomic: GGGGAGCGCCTACACC-ACCATTGCCGCCGACGCCATCGCCCGCTTCCAGgcaagcaact ... atggtcgcagAGGTTGCTGGATAAGAGGGTCGTATTTATTACCGGAACAGATGAGCATGGC