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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctaatcatgtgatttcaattgttcgaacttttctacatgatagtatgagccacttctcattgggaatttcctgctccttgttatcttatttgtttcagGTAGCGTACTTGCTATGCTTGAAGCTGTAATGTCTTTTGTTCCAGTGGACAAGATCGCCGTCCATTTCCATGACACATACGGCCAAGCCCTTGCCAACAT

Basic information

species Oryza sativa
transcript LOC_Os12g04020.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04020.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G095141_T01 (Zea mays), 3'ss of exon 5
-------------------------tgctaatc---atgtgatttcaattgttcgaacttttctacatgatagtatgagccacttctcattgggaat--ttcctgctccttgttatcttatttgtttcagGTAGCGTACTTGCTATGCTTGAAGCTGTAATGTCTTTTGTTCCAGTGGACAAGATCGCCGTCCATTTCCATGACACATACGGCCAAGCCCTTGCCAACAT
                         |||||  |   |   | |      | |  |   ||||||  |   ||    |||  ||    ||      ||  |  ||||   |||  | | | | ||  |||||||||||  ||||||||||| ||||||| ||||| ||||| || ||||||||||| ||||| |||||||| || || ||||| || ||||||||||||||
gtgtactactggttctctctgcctatgctatgccgaacccgttcgtggctctcagtcgttttctggacagtacgtggagagaccggccaaaaactatactcactgcgatttgcaaacgtctctgcctcagGTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACAAGATTGCCGTTCATTTCCACGATACGTACGGGCAGGCCCTTGCCAACAT

upper sequence: LOC_Os12g04020.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G095141_T03 (Zea mays), 3'ss of exon 7
-----------------------tgctaatc---atgtgatttcaattgttcgaacttttctacatgatagtatgagccacttctcattgggaat--ttcctgctccttgttatcttatttgtttcagGTAGCGTACTTGCTATGCTTGAAGCTGTAATGTCTTTTGTTCCAGTGGACAAGATCGCCGTCCATTTCCATGACACATACGGCCAAGCCCTTGCCAACAT
                       |||||  |   |   | |      | |  |   ||||||  |   ||    |||  ||    ||      ||  |  ||||   |||  | | | | ||  |||||||||||  ||||||||||| ||||||| ||||| ||||| || ||||||||||| ||||| |||||||| || || ||||| || ||||||||||||||
gtactactggttctctctgcctatgctatgccgaacccgttcgtggctctcagtcgttttctggacagtacgtggagagaccggccaaaaactatactcactgcgatttgcaaacgtctctgcctcagGTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACAAGATTGCCGTTCATTTCCACGATACGTACGGGCAGGCCCTTGCCAACAT

upper sequence: LOC_Os12g04020.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 3'ss of exon 6
-tgctaat-catgtgatttcaattgttcgaacttttctacatgatagtatgagccacttctcattgggaatttcctgctccttgttatcttatttgtttcagGTAGCGTACTTGCTATGCTTGAAGCTGTAATGTCTTTTGTTCCAGTGGACAAGATCGCCGTCCATTTCCATGACACATACGGCCAAGCCCTTGCCAACAT
    ||||  || ||||      |||    | ||   || |||  |||| ||   |      |      ||   ||      |    |  | | ||| |||||   | |  || |||||||||||||||||||| || ||||||| || || ||| | || ||||| ||||||||||| || || ||  | ||| | || ||
agcttaatgtatttgatagtttgtgtcaataattagttaaatg-cagta-gaattaagaaagagaaaccatcatctataatcttcatttatttatgtatcagGCGCCATTGTTCCTATGCTTGAAGCTGTAATGGCTGTTGTTCCTGTTGAGAAGCTTGCTGTCCACTTCCATGACACTTATGGGCAGTCTCTTCCAAATAT

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|88985612|gb|CI016321.1|CI016321
EST:     CGGAGATCTCACTCGGAGACACGATTGGTGTTGGTACACCAG                         GTAGCGTACTTGCTATGCTTGAAGCTGTAATGTCTTTTGTTCCAGTGGACA
genomic: CGGAGATCTCACTCGGAGACACGATTGGTGTTGGTACACCAGgtattgattt ... tttgtttcagGTAGCGTACTTGCTATGCTTGAAGCTGTAATGTCTTTTGTTCCAGTGGACA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgagccacttctcattgggaatttcctgctccttgttatcttatttgtttcagGTAGCGTACTTGCTATGCTTGAAGCTGTAATGTCTTTTGTTCCAGTGGACAAGATCGCCGTCCATTTCCATGACACATACGGCCAAGCCCTTGCCAACAT
                                        tcttattt  CT-rich tract
                                     ttatcttatttgttt  TA-rich tract