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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctcaccagagggtattcattatgaagcaaactattagttcattgtaattgttattaccttttcttttagaagtcaatcgtcatcacttgcagGGCTGGAAATCAGGCGCTGTAACCACTTTAGGCCGAGGTGGCAGTGACTTGACTGCTACAACCATTGGTAAAGCCCTGGGGTTGAGAGAAATTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g70300.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G300862_T02 (Zea mays), 3'ss of exon 6
gtattctcaccagagggtattcattatgaagcaaactattagttcattgtaattgttattaccttttcttttagaagtcaatcgtcatcacttgcagGGCTGGAAATCAGGCGCTGTAACCACTTTAGGCCGAGGTGGCAGTGACTTGACTGCTACAACCATTGGTAAAGCCCTGGGGTTGAGAGAAATTCAG
                |||||  | ||  | ||||| |||  |||||      ||     || | ||   |       |||  | ||||||||||||||||||||||| || |||||||| ||||||||||||||||| |||||||||||||||||||||||||                             
----------------gtatt--tcatcga-caaacaatttcttcatc---catgaggcaacttgtttactg------caactgccatcacttgcagGGCTGGAAATCTGGTGCTGTAACTACTTTAGGCCGAGGTGGTAGTGACTTGACTGCTACAACCATTG-----------------------------

upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G300862_T05 (Zea mays), 3'ss of exon 5
gtattctcaccagagggtattcattatgaagcaaactattagttcattgtaattgttattaccttttcttttagaagtcaatcgtcatcacttgcagGGCTGGAAATCAGGCGCTGTAACCACTTTAGGCCGAGGTGGCAGTGACTTGACTGCTACAACCATTGGTAAAGCCCTGGGGTTGAGAGAAATTCAG
                |||||  | ||  | ||||| |||  |||||      ||     || | ||   |       |||  | ||||||||||||||||||||||| || |||||||| ||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||  ||||||||||||||
----------------gtatt--tcatcga-caaacaatttcttcatc---catgaggcaacttgtttactg------caactgccatcacttgcagGGCTGGAAATCTGGTGCTGTAACTACTTTAGGCCGAGGTGGTAGTGACTTGACTGCTACAACCATTGGTAAAGCCTTGGGACTGAGAGAAATTCAG

upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G700866_T02 (Zea mays), 3'ss of exon 7
-gtattc-tcaccagagggtattcattatgaagcaaactattagtt--cattgtaattgttattaccttttcttttagaagtcaatcgtcatcacttgcagGGCTGGAAATCAGGCGCTGTAACCACTTTAGGCCGAGGTGGCAGTGACTTGACTGCTACAACCATTGGTAAAGCCCTGGGGTTGAGAGAAATTCAG
  ||    |    |  |||| | | |    | | |    ||       || | |  |  |   |       ||| |  |   ||| || ||||||||||||||||||||||| || ||| |||| |||||||||| |||||| || ||||||| ||||| |||||||||||||||| ||||  ||||||||||||||
gatacctgttgttactgggt-tccttgggaaggtatctcatcgacaaacaatttcttcatccatgagacaacttgtttactgcaaccgccatcacttgcagGGCTGGAAATCTGGTGCTATAACTACTTTAGGCCAAGGTGGTAGCGACTTGATTGCTATAACCATTGGTAAAGCCTTGGGACTGAGAGAAATTCAG

upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G866647_T01 (Zea mays), 3'ss of exon 2
gtattctcaccagagggtat-tcattatgaagcaaactattagttcattgtaattgttattaccttttcttttagaagtcaatcgtcatcacttgcagGGCTGGAAATCAGGCGCTGTAACCACTTTAGGCCGAGGTGGCAGTGACTTGACTGCTACAACCATTGGTAAAGCCCTGGGGTTGAGAGAAATTCAG
                |||| |||||   || |||  | ||  | |||             | ||| | |  |      ||| || ||||||||||||||||||||||| || |||||||| ||||||||||||||||| || |||||||||||||||||||||||||||||| ||||  ||||||||||||||
----------------gtatctcattgacaaacaatttcttcatccatgagg--------caacttgtttactg-----caaccgccatcacttgcagGGCTGGAAATCTGGTGCTGTAACTACTTTAGGCCGAGGTGGTAGCGACTTGACTGCTACAACCATTGGTAAAGCCTTGGGACTGAGAGAAATTCAG

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|58669471|gb|CK058157.1|CK058157
EST:     ACTGGATTCGTGATCCAGCGATACCTATTGTTACTGGGTTCCTTGGGAAG                         GGCTGGAAATCAGGCGCTGTAACCACTTTAGGCCGAGGTGGCAGTGACTTG
genomic: ACTGGATTCGTGATCCAGCGATACCTATTGTTACTGGGTTCCTTGGGAAGgtattctcac ... tcacttgcagGGCTGGAAATCAGGCGCTGTAACCACTTTAGGCCGAGGTGGCAGTGACTTG
EST: gi|29669913|gb|CB666188.1|CB666188
EST:     ACTGGATTCGTGATCCAGCGATACCTATTGTTACTGGGTTCCTTGGGAAG                         GGCTGGAAATCAGGCGCTGTAACCACTTTAGGCCGAGGTGGCAGTGACTTG
genomic: ACTGGATTCGTGATCCAGCGATACCTATTGTTACTGGGTTCCTTGGGAAGgtattctcac ... tcacttgcagGGCTGGAAATCAGGCGCTGTAACCACTTTAGGCCGAGGTGGCAGTGACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcattgtaattgttattaccttttcttttagaagtcaatcgtcatcacttgcagGGCTGGAAATCAGGCGCTGTAACCACTTTAGGCCGAGGTGGCAGTGACTTGACTGCTACAACCATTGGTAAAGCCCTGGGGTTGAGAGAAATTCAG
     tgtaattgttatta  TA-rich tract