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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtaaacaacctttgtcaactactttcaaagctcgttggtgatctttaccttattacattcatttcagccacaaaccatttttcacaaattatggttgagcaacttattgcttgatatgctctgtaagtaatgcattatatggcaccgtgaagcatatcatcatttcatctattgcagGCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG

Basic information

species Oryza sativa
transcript LOC_Os05g28180.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28180.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 17
gcaagtaaacaacctttgtcaactactttcaaagctcgttggtgatctttaccttattacattcatttcagccacaaaccatttttcacaaattatggttgagcaacttattgcttgatatgctctgtaagtaatgcattatatggcaccgtgaagcatatcatcatttcatctattgcagGCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG
                                                                    |   |   |  || |       || |||  | ||| |  |  || | || |  |   | ||| |       | | | | ||     | || || |||||   |||| | |||||| ||||||||||| |||||||| | ||||||||||||| | || || |||||||| | ||| ||||| || |||||||||||||| ||||| ||  ||
------------------------------------------------------------------ccctctcttgagacactg-----gaaatatattagagaaggtcgttacctgcttag---tataaatg------tgtgtagaac-acacatcaaataatcatacgatctttggcagGCGCACTGGATTGGTAAGAACTACTTCAAAAGAGGACCTGCTGGAAATGATATTCACAGAACCAATGTACCGCACATCAGGGTTCAATTTAGAGAGATG
















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|29675538|gb|CB671813.1|CB671813
EST:     AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAG                         GCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
genomic: AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAGgcaagtaaac ... tctattgcagGCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
EST: gi|27548799|gb|CA767547.2|CA767547
EST:     AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAG                         GCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
genomic: AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAGgcaagtaaac ... tctattgcagGCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
EST: gi|29638453|gb|CB643462.1|CB643462
EST:     AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAG                         GCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
genomic: AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAGgcaagtaaac ... tctattgcagGCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
EST: gi|86481338|gb|CI123971.1|CI123971
EST:     CTATCAATCAGGGTTTTCACATGCTCTCAAG                         GCACACTGGATTGCCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
genomic: CTATCAATCAGGGTTTTCACATGCTCTCAAGgcaagtaaac ... tctattgcagGCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
EST: gi|29637475|gb|CB642484.1|CB642484
EST:     AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAG                         GCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
genomic: AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAGgcaagtaaac ... tctattgcagGCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
EST: gi|87022773|gb|CI269709.1|CI269709
EST:     AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAG                         GCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
genomic: AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAGgcaagtaaac ... tctattgcagGCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtaatgcattatatggcaccgtgaagcatatcatcatttcatctattgcagGCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG
                                        tttcatct  CT-rich tract
           attatat  TA-rich tract