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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattctacttctatcaggccatctttatgcatttattttttcttgagctctaagtttcttttttctggagctctaagttttgtgtattgtccatgttcagGCCTTTCTGGAGCAAAGACTTGAGGAGCTTGAGACAGTGGAAGATATAAATCATCTAATTTTCACTGATTCTGATATAGCAGTGGTTACTGATCTTGGAC

Basic information

species Oryza sativa
transcript LOC_Os06g37430.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g37430.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G350001_T01 (Zea mays), 3'ss of exon 9
-----------------------------------------------cattctacttctatcaggccatctttatgcatttattttttcttgagctctaagt-ttcttttttctg-gagctctaagttt-tgtgtattgtcc--atgttcagGCCTTTCTGGAGCAAAGACTTGAGGAGCTTGAGACAGTGGAAGATATAAATCATCTAATTTTCACTGATTCTGATATAGCAGTGGTTACTGATCTTGGAC
                                                  || |  |   | | |  |||   ||| |||  |  | || | | || || |  || ||||  |||  ||   ||  ||| ||| | || |||  || || |||| |||||||||||||  |||| |||  |||| |    |||     | |||||| |  |||| |||||||| |||||||||||||||  |||||||||||
gtaagtgtatcggcttcatttagatcataaaattttatgcatatgctttctcaaaattacttatgtgatc--catgtattactgctatcatcatctttatgcattattttcactgtaagagttatatttatgtatcttatcctcatatttagGCATTTCTGGAGCAAAAGCTTGTGGAATTTGATAGGACGGAGAGGCTGAATCATTTTGTTTTAACTGATTCCGATATAGCAGTGGTTGATGATCTTGGAC

upper sequence: LOC_Os06g37430.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G143688_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------cattctacttctatcaggccatctttatgcatttattttttcttgagctctaagtttctttttt--ctg-gagctctaagttt-tgtgtattgtcc--atgttcagGCCTTTCTGGAGCAAAGACTTGAGGAGCTTGAGACAGTGGAAGATATAAATCATCTAATTTTCACTGATTCTGATATAGCAGTGGTTACTGATCTTGGAC
                                                  || |  |   | | |  |||   ||| |||  |  | || | | || || |  |  ||||   |||  ||   ||  ||| ||| | || |||  || || |||| |||||||||||||  |||| |||  |||| |    |||     | |||||| |  |||| |||||||| |||||||||||||||  |||||||||||
gtaagtgtatcggcttcatttagatcattaaattttctgcatatgctttctcaaaattacttatgtgatc--catgtattactgctatcatcatctttatgcattattttcaactgtaagagttatatttatgtatcttatcctcatatttagGCATTTCTGGAGCAAAAGCTTGTGGAATTTGATAGGACGGAGAGGTTGAATCATTTTGTTTTAACTGATTCCGATATAGCAGTGGTTGATGATCTTGGAC

upper sequence: LOC_Os06g37430.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G342254_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------cattctacttctatcaggccatctttatgcatttattttttcttgagctctaagtttcttttt----tctggagctctaagttttgtgtattgtcc--atgttcagGCCTTTCTGGAGCAAAGACTTGAGGAGCTTGAGACAGTGGAAGATATAAATCATCTAATTTTCACTGATTCTGATATAGCAGTGGTTACTGATCTTGGAC
                                               |  || |  |   | | |  |||   ||| |||  |  | || | | || || |  |  ||||    | |     |   | || ||| | || |||  || || |||| |||||||||||||  |||| |||  |||| |    |||     | |||||| |  |||| |||||||| |||||||||||||||  |||||||||||
gtaagtgtatcggcttcatttagatcattaaattttctgcatatggtctctcaaaattacttatgtgatc--catgtattactgctatcatcatctttatgcattattttgaactgtaagagttatatttatgtatcttatcctcatatttagGCATTTCTGGAGCAAAAGCTTGTGGAATTTGATAGGACGGAGAGGTTGAATCATTTTGTTTTAACTGATTCCGATATAGCAGTGGTTGATGATCTTGGAC

upper sequence: LOC_Os06g37430.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G038667_T03 (Zea mays), 3'ss of exon 5
-------------------------------------------------------cattctacttctatcaggccatctttatgcatttattttttcttgagctctaagtttctttttt--ctg-gagctctaagttt-tgtgtattgtcc--atgttcagGCCTTTCTGGAGCAAAGACTTGAGGAGCTTGAGACAGTGGAAGATATAAATCATCTAATTTTCACTGATTCTGATATAGCAGTGGTTACTGATCTTGGAC
                                                          || |  |   | | |  |  || ||| |||  | || || | | || || |  |  ||||   |||  ||   ||  ||| | | | || |||  || | ||||| |||||||||||||  |||| |||  |||| |   ||||     | |||||| |  |||| |||||||| |||||||||||||||  |||||||||||
gtaagtccatcggctattcggcttcatttagatcattaaattttgtgcatatgctttctcaaaattacttatgtga--ttcatgtattactgttatcgtcatctttatgcattattttcaactgcaagaattatatttatctatcttatcctcatatccagGCATTTCTGGAGCAAAAGCTTGTGGAATTTGATAGGATGGAGAGGTTGAATCATTTTGTTTTAACTGATTCCGATATAGCAGTGGTTGGTGATCTTGGAC

upper sequence: LOC_Os06g37430.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G42210.1 (Glycine max), 3'ss of exon 2
cattctacttctatcaggccatctttatgcatttattttttcttgagctctaagtttcttttttctggagctcta-agttttgtgtattgtccatgttcagGCCTTTCTGGAGCAAAGACTTGAGGAGCTT------GAGACAGTGGAAGATATAAATCATCTAATTTTCACTGATTCTGATATAGCAGTGGTTACTGATCTTGGAC----
  || |  || |||||        ||||   |  ||  | | | ||  | |||  || |  ||  |  | ||  | |   || ||| ||     | | ||| ||||| | ||   ||| ||  || | |||       |||      || |||| | ||||   || |||||||||||||||||||||||||||  |||| | || |    
--ttttttttttatca--------ttataggtg-atggtgtttagaattttaaaattttaattctttaaactaaataaccttatgttttccttctttacagacctttttagAAACAAGGCTCCAGAATCTTTCTCAGAAGAAGCCAAAAAATATCACTCATTACATCTTCACTGATTCTGATATAGCAGTGGTTGATGATTTAGGGCAGAT

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|29671600|gb|CB667875.1|CB667875
EST:     GAAATTATTCTCGAGGAAACTTGATGTTTCAGAGGATCAGGTCCTACATA                         GCCTTTCTGGAGCAAAGACTTGAGGAGCTTGAGACAGTGGAAGATATAAAT
genomic: GAAATTATTCTCGAGGAAACTTGATGTTTCAGAGGATCAGGTCCTACATAgtaagtctgt ... ccatgttcagGCCTTTCTGGAGCAAAGACTTGAGGAGCTTGAGACAGTGGAAGATATAAAT
EST: gi|325493846|gb|JG458370.1|JG458370
EST:     GATGTTTCAGAGGATCAGGTCCTACATA                         GCCTTTCTGGAGCAAAGACTTGAGGAGCTTGAGACAGTGGAAGATATAAAT
genomic: GATGTTTCAGAGGATCAGGTCCTACATAgtaagtctgt ... ccatgttcagGCCTTTCTGGAGCAAAGACTTGAGGAGCTTGAGACAGTGGAAGATATAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctctaagtttcttttttctggagctctaagttttgtgtattgtccatgttcagGCCTTTCTGGAGCAAAGACTTGAGGAGCTTGAGACAGTGGAAGATATAAATCATCTAATTTTCACTGATTCTGATATAGCAGTGGTTACTGATCTTGGAC
     taagtttctttttt  TA-rich tract