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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaaaatagcacacaacatatgctctattaaggtcaacatcatgctatgactattacatataactgaaattgatttaatcttgtactaaatcgatgcagGTTACTGCTGCTCAAATCAAGGCTGAAATGGAGAAGACTTTGCGGTGGCTTGTCCCAATTGCAAATAACACCACCAAGTATTATAAGCTATCTTAATAGA

Basic information

species Oryza sativa
transcript LOC_Os01g65330.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G148773_T01 (Zea mays), 3'ss of exon 9
gtatgcaaaatagcacacaaca-tatgctctattaaggtcaacatcatgctatgactattacatataactgaaa--ttgatttaatcttgtactaaatcgatgcagGTTACTGCTGCTCAAATCAAGGCTGAAATGGAGAAGACTTTGCGGTGGCTTGTCCCAATTGCAAATAACACCACCAAGTATTATAAGCTATCTTAATAGA
      | ||    |  ||| | |||  |  |  |  |  |  |  ||| ||    ||    || ||| || ||  || ||  || ||  | ||  ||   || || |||||| | ||||||||||||||||||||||||||||  |||| ||||||| ||| ||||||| ||||||||||||                       
-----aagaactaaaatcaatactatattggaacagagggagtactatgttacatgtaa-gtatgtaattgtaagtttaatgaaagctattgctggatttgtgtagCTTACTGTTTCTCAAATCAAGGCTGAAATGGAGAAGACCCTGCGATGGCTTGCCCCTATTGCAAGTAACACCACCAA-----------------------

upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G046846_T01 (Zea mays), 3'ss of exon 10
gtatgcaaaatagcacaca----------acatatgctctat-taaggtcaacatcatgctatgactattacatataa--------ctgaaa--ttgatttaatcttgtactaaatcgatgcagGTTACTGCTGCTCAAATCAAGGCTGAAATGGAGAAGACTTTGCGGTGGCTTGTCCCAATTGCAAATAACACCACCAAGTATTATAAGCTATCTTAATAGA
||||||   ||  ||| ||          |   | |    || ||  ||||||||| | |||||  | | |||| |||         || ||  || ||  || ||| | || |||   || || |||||| | ||||||||||||||||||||||||||||  |||||||||||||||| ||||||| ||||||||||||                       
gtatgcgggatgacacccatgcttgaaaaatgaaagtaggatgtagagtcaacatcgtactatgtttgtgacatgtaagtatgtaattggaagtttaatgcaagcttttgctgaatttgtgtagCTTACTGTTTCTCAAATCAAGGCTGAAATGGAGAAGACCCTGCGGTGGCTTGTCCCTATTGCAAGTAACACCACCAA-----------------------

upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 9
-----------------------------------------------------------gtatgcaaaatagcacacaacatatgctctattaaggtca-acatcatgctatgactattacatataactgaaattgatttaatcttgtactaaatcgatgcagGTTACTGCTGCTCAAATCAAGGCTGAAATGGAGAAGACTTTGCGGTGGCTTGTCCCAATTGCAAATAACACCACCAAGTATTATAAGCTATCTTAATAGA
                                                              ||  |    |  | ||  |     |  ||| || | |  | | ||  | ||     | |||  | || |||   |||   ||||| ||| |       ||| ||||   | | |||||||| |||||||||||||| |||||||  |||||||| || |||||    ||||| |||||                       
gtatttattacacattcggctcttctttgttgcactttaaaagcaaataggtatttattacttgggatgctggtcccactagtactttcattgagataacgcctaatattttgctctgtgcatgca-cttaaaacaattc--tcttg-actgatgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA-----------------------

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|29680203|gb|CB676478.1|CB676478
EST:     TAAAATCGTCCTTGCGTTCTAAGGTGAATTCATTTGTGGTCAATGAAGAG                         GTTACTGCTGCTCAAATCAAGGCTGAAATGGAGAAGACTTTGCGGTGGCTT
genomic: TAAAATCGTCCTTGCGTTCTAAGGTGAATTCATTTGTGGTCAATGAAGAGgtatgcaaaa ... atcgatgcagGTTACTGCTGCTCAAATCAAGGCTGAAATGGAGAAGACTTTGCGGTGGCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatgactattacatataactgaaattgatttaatcttgtactaaatcgatgcagGTTACTGCTGCTCAAATCAAGGCTGAAATGGAGAAGACTTTGCGGTGGCTTGTCCCAATTGCAAATAACACCACCAAGTATTATAAGCTATCTTAATAGA
                                       tactaaa  putative branch site (score: 1)
       tattacatataactga  TA-rich tract