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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtcagtcactgttgttacctgctgattgcaaaaccatctcttctgataatgatattcacaaccagttgttaaaaaaaaacagagagaatataatcacatccagttcatagtgccttctaaaatcaacctctcatttctccgaaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGACGGATCAACGAAAAATACCATCTGATCAACTCGAGGAACGGGATGGTAC

Basic information

species Oryza sativa
transcript LOC_Os06g47130.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g47130.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G140443_T02 (Zea mays), 3'ss of exon 11
gtcagtcagtcactgttgttacctgctgattgcaaaaccatctcttctgataatgatattcacaaccagttgttaaaaaaaaacagagagaatataatcacatccagttcatagtgccttctaaaatcaacctctcattt-ctccgaaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGACGGATCAACGAAAAATACCATCTGATCAACTCGAGGAACGGGATGGTAC
                                                                                          ||   |  ||  || | |   |  || || | | ||  |||   |   |  |        || ||||||||  ||||||||||| |||||||||| ||||| || ||||||||||| ||||||||||| || ||||| || |||||||| |||||||||||| |||
----------------------------------------------------------------------------------------gcaagtcacgcagctctaatctttgctgtctgccataactaactcatagctgacggtccgtcttccagGAATCGCTGGGGCATGTGAATATAAACCTGGTGGATGTGGTGAACAACGGCCGGATCAACGAGAAGTACCACCTCATCAACTCCAGGAACGGGATGATAC

upper sequence: LOC_Os06g47130.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA10G35410.1 (Glycine max), 3'ss of exon 11
gtcagtcagtcactgttgttacctgctgattgcaaaaccatctcttctgataatgatattcacaaccagttgttaaaaaaaaacagagagaatataatcacatccagttcatagtgcct-tctaaaatcaacctctcatttctccgaaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGACGGATCAACGAAAAATACCATCTGATCAACTCGAGGAACGGGATGGTAC
                                             |  |||||    | || ||   | |  | ||      |   |  |  ||| | |   |    |||||| | ||  | | | |  ||  | |||| | |  |       ||||||||||||||||||||||| || ||||||   || || ||| |||| || || || ||||| || |||||||| || || || ||||| ||  || | |
--------------------------------------------attcgataacttcaatc-catgtactcatcaatctgttaattaccgtttattagcttgtt---ttcataattccaatgtgatactaatat-tcatatttatg-------cagGAATCATTGGGGCATGTGGAGATTAACCTAAGAGATGTGGTGCACAATGGTCGCATTAACGATAAGTACCATCTAATAAATTCAAGGAATGGAGTGATGC
















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|88505624|gb|CI433130.1|CI433130
EST:     GTGGGCTCCGGCTTCCCTTCCGCAATAAG                         GAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
genomic: GTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagt ... aaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
EST: gi|88281509|gb|CI402905.1|CI402905
EST:     TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAG                         GAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
genomic: TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagt ... aaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
EST: gi|88470704|gb|CI407975.1|CI407975
EST:     TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAG                         GAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
genomic: TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagt ... aaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
EST: gi|88516986|gb|CI444640.1|CI444640
EST:     TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAG                         GAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
genomic: TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagt ... aaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
EST: gi|88486628|gb|CI423899.1|CI423899
EST:     TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAG                         GAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
genomic: TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagt ... aaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
EST: gi|4715980|gb|AU057096.1|AU057096
EST:     TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAG                         GAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
genomic: TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagt ... aaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
EST: gi|4715981|gb|AU057097.1|AU057097
EST:     TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAG                         GAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
genomic: TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagt ... aaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
EST: gi|88478208|gb|CI415479.1|CI415479
EST:     CGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAG                         GAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
genomic: CGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagt ... aaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catccagttcatagtgccttctaaaatcaacctctcatttctccgaaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGACGGATCAACGAAAAATACCATCTGATCAACTCGAGGAACGGGATGGTAC
                  ttctaaa  putative branch site (score: 2)
                  ttctaaaat  TA-rich tract